diff --git a/analytics/lib/counts.py b/analytics/lib/counts.py
index 382813f479..b0b3e06722 100644
--- a/analytics/lib/counts.py
+++ b/analytics/lib/counts.py
@@ -447,7 +447,13 @@ def count_message_by_user_query(realm: Optional[Realm]) -> QueryFn:
     if realm is None:
         realm_clause: Composable = SQL("")
     else:
-        realm_clause = SQL("zerver_userprofile.realm_id = {} AND").format(Literal(realm.id))
+        # We limit both userprofile and message so that we only see
+        # users from this realm, but also get the performance speedup
+        # of limiting messages by realm.
+        realm_clause = SQL(
+            "zerver_userprofile.realm_id = {} AND zerver_message.realm_id = {} AND"
+        ).format(Literal(realm.id), Literal(realm.id))
+    # Uses index: zerver_message_realm_date_sent (or the only-date index)
     return lambda kwargs: SQL(
         """
     INSERT INTO analytics_usercount
@@ -474,7 +480,13 @@ def count_message_type_by_user_query(realm: Optional[Realm]) -> QueryFn:
     if realm is None:
         realm_clause: Composable = SQL("")
     else:
-        realm_clause = SQL("zerver_userprofile.realm_id = {} AND").format(Literal(realm.id))
+        # We limit both userprofile and message so that we only see
+        # users from this realm, but also get the performance speedup
+        # of limiting messages by realm.
+        realm_clause = SQL(
+            "zerver_userprofile.realm_id = {} AND zerver_message.realm_id = {} AND"
+        ).format(Literal(realm.id), Literal(realm.id))
+    # Uses index: zerver_message_realm_date_sent (or the only-date index)
     return lambda kwargs: SQL(
         """
     INSERT INTO analytics_usercount
@@ -523,7 +535,10 @@ def count_message_by_stream_query(realm: Optional[Realm]) -> QueryFn:
     if realm is None:
         realm_clause: Composable = SQL("")
     else:
-        realm_clause = SQL("zerver_stream.realm_id = {} AND").format(Literal(realm.id))
+        realm_clause = SQL(
+            "zerver_stream.realm_id = {} AND zerver_message.realm_id = {} AND"
+        ).format(Literal(realm.id), Literal(realm.id))
+    # Uses index: zerver_message_realm_date_sent (or the only-date index)
     return lambda kwargs: SQL(
         """
     INSERT INTO analytics_streamcount
diff --git a/analytics/views/installation_activity.py b/analytics/views/installation_activity.py
index e713658b5d..4bfd97e369 100644
--- a/analytics/views/installation_activity.py
+++ b/analytics/views/installation_activity.py
@@ -39,6 +39,7 @@ if settings.BILLING_ENABLED:
 
 
 def get_realm_day_counts() -> Dict[str, Dict[str, Markup]]:
+    # Uses index: zerver_message_date_sent_3b5b05d8
     query = SQL(
         """
         select
diff --git a/analytics/views/realm_activity.py b/analytics/views/realm_activity.py
index ffcdbf6769..d5246bda09 100644
--- a/analytics/views/realm_activity.py
+++ b/analytics/views/realm_activity.py
@@ -163,6 +163,7 @@ def sent_messages_report(realm: str) -> str:
         "Bots",
     ]
 
+    # Uses index: zerver_message_realm_date_sent
     query = SQL(
         """
         select
@@ -188,6 +189,8 @@ def sent_messages_report(realm: str) -> str:
                 r.string_id = %s
             and
                 date_sent > now() - interval '2 week'
+            and
+                m.realm_id = r.id
             group by
                 date_sent::date
             order by
diff --git a/corporate/tests/test_stripe.py b/corporate/tests/test_stripe.py
index b17388eaa5..321d9ef4f5 100644
--- a/corporate/tests/test_stripe.py
+++ b/corporate/tests/test_stripe.py
@@ -2550,7 +2550,7 @@ class StripeTest(StripeTestCase):
         )
         sender = get_system_bot(settings.NOTIFICATION_BOT, user.realm_id)
         recipient_id = self.example_user("desdemona").recipient_id
-        message = Message.objects.filter(sender=sender.id).first()
+        message = Message.objects.filter(realm_id=realm.id, sender=sender.id).first()
         assert message is not None
         self.assertEqual(message.content, expected_message)
         self.assertEqual(message.recipient.type, Recipient.PERSONAL)
diff --git a/tools/generate-integration-docs-screenshot b/tools/generate-integration-docs-screenshot
index 52e761fd7e..b8678eda44 100755
--- a/tools/generate-integration-docs-screenshot
+++ b/tools/generate-integration-docs-screenshot
@@ -139,7 +139,7 @@ def send_bot_mock_message(
     bot: UserProfile, integration: Integration, fixture_path: str, config: BaseScreenshotConfig
 ) -> None:
     # Delete all messages, so new message is the only one it's message group
-    Message.objects.filter(sender=bot).delete()
+    Message.objects.filter(realm_id=bot.realm_id, sender=bot).delete()
     data, _, _ = get_fixture_info(fixture_path)
 
     assert bot.bot_owner is not None
@@ -166,7 +166,7 @@ def send_bot_payload_message(
     bot: UserProfile, integration: WebhookIntegration, fixture_path: str, config: ScreenshotConfig
 ) -> bool:
     # Delete all messages, so new message is the only one it's message group
-    Message.objects.filter(sender=bot).delete()
+    Message.objects.filter(realm_id=bot.realm_id, sender=bot).delete()
     data, json_fixture, fixture_name = get_fixture_info(fixture_path)
 
     headers = get_requests_headers(integration.name, fixture_name)
@@ -217,7 +217,7 @@ def send_bot_payload_message(
 
 
 def capture_last_message_screenshot(bot: UserProfile, image_path: str) -> None:
-    message = Message.objects.filter(sender=bot).last()
+    message = Message.objects.filter(realm_id=bot.realm_id, sender=bot).last()
     realm = get_realm("zulip")
     if message is None:
         print(f"No message found for {bot.full_name}")
diff --git a/tools/semgrep.yml b/tools/semgrep.yml
index 00fda02b5b..d1ee2c6285 100644
--- a/tools/semgrep.yml
+++ b/tools/semgrep.yml
@@ -17,6 +17,23 @@ rules:
       include:
         - zerver/views/
 
+  - id: limit-message-filter
+    patterns:
+      - pattern: Message.objects.filter(...)
+      - pattern-not: Message.objects.filter(..., realm=..., ...)
+      - pattern-not: Message.objects.filter(..., realm_id=..., ...)
+      - pattern-not: Message.objects.filter(..., realm_id__in=..., ...)
+      - pattern-not: Message.objects.filter(..., id=..., ...)
+      - pattern-not: Message.objects.filter(..., id__in=..., ...)
+      - pattern-not: Message.objects.filter(..., id__lt=..., ...)
+      - pattern-not: Message.objects.filter(..., id__gt=..., ...)
+    message: "Set either a realm limit or an id limit on Message queries"
+    languages: [python]
+    severity: ERROR
+    paths:
+      exclude:
+        - "**/migrations/"
+
   - id: dont-import-models-in-migrations
     patterns:
       - pattern-not: from zerver.lib.redis_utils import get_redis_client
diff --git a/zerver/actions/create_user.py b/zerver/actions/create_user.py
index 4da6872adc..6031f9bb62 100644
--- a/zerver/actions/create_user.py
+++ b/zerver/actions/create_user.py
@@ -181,7 +181,12 @@ def add_new_user_history(user_profile: UserProfile, streams: Iterable[Stream]) -
     # Start by finding recent messages matching those recipients.
     cutoff_date = timezone_now() - ONBOARDING_RECENT_TIMEDELTA
     recent_message_ids = set(
-        Message.objects.filter(recipient_id__in=recipient_ids, date_sent__gt=cutoff_date)
+        Message.objects.filter(
+            # Uses index: zerver_message_realm_recipient_id
+            realm_id=user_profile.realm_id,
+            recipient_id__in=recipient_ids,
+            date_sent__gt=cutoff_date,
+        )
         .order_by("-id")
         .values_list("id", flat=True)[0:MAX_NUM_ONBOARDING_MESSAGES]
     )
diff --git a/zerver/actions/invites.py b/zerver/actions/invites.py
index 24a0649693..b0fd6d29ae 100644
--- a/zerver/actions/invites.py
+++ b/zerver/actions/invites.py
@@ -134,7 +134,11 @@ def too_many_recent_realm_invites(realm: Realm, num_invitees: int) -> bool:
         not estimated_sent["messages"]
         # Only after we've done the rough-estimate check, take the
         # time to do the exact check:
-        and not Message.objects.filter(realm=realm, sender__is_bot=False).exists()
+        and not Message.objects.filter(
+            # Uses index: zerver_message_realm_sender_recipient (prefix)
+            realm=realm,
+            sender__is_bot=False,
+        ).exists()
     ):
         warning_flags.append("no-messages-sent")
 
diff --git a/zerver/actions/message_delete.py b/zerver/actions/message_delete.py
index 7777793bba..6aca536b0a 100644
--- a/zerver/actions/message_delete.py
+++ b/zerver/actions/message_delete.py
@@ -59,7 +59,10 @@ def do_delete_messages(realm: Realm, messages: Iterable[Message]) -> None:
 
 def do_delete_messages_by_sender(user: UserProfile) -> None:
     message_ids = list(
-        Message.objects.filter(sender=user).values_list("id", flat=True).order_by("id")
+        # Uses index: zerver_message_realm_sender_recipient (prefix)
+        Message.objects.filter(realm_id=user.realm_id, sender=user)
+        .values_list("id", flat=True)
+        .order_by("id")
     )
     if message_ids:
         move_messages_to_archive(message_ids, chunk_size=retention.STREAM_MESSAGE_BATCH_SIZE)
diff --git a/zerver/actions/message_edit.py b/zerver/actions/message_edit.py
index c62a17f671..ff64b1a9b2 100644
--- a/zerver/actions/message_edit.py
+++ b/zerver/actions/message_edit.py
@@ -611,7 +611,7 @@ def do_update_message(
 
         assert target_stream.recipient_id is not None
         target_topic_has_messages = messages_for_topic(
-            target_stream.recipient_id, target_topic
+            realm.id, target_stream.recipient_id, target_topic
         ).exists()
 
     if propagate_mode in ["change_later", "change_all"]:
@@ -804,6 +804,7 @@ def do_update_message(
             # unless the topic has thousands of messages of history.
             assert stream_being_edited.recipient_id is not None
             unmoved_messages = messages_for_topic(
+                realm.id,
                 stream_being_edited.recipient_id,
                 orig_topic_name,
             )
@@ -1041,7 +1042,7 @@ def do_update_message(
             # it reuses existing logic, which is good for keeping it
             # correct as we maintain the codebase.
             preexisting_topic_messages = messages_for_topic(
-                stream_for_new_topic.recipient_id, new_topic
+                realm.id, stream_for_new_topic.recipient_id, new_topic
             ).exclude(id__in=[*changed_message_ids, resolved_topic_message_id])
 
             visible_preexisting_messages = bulk_access_messages(
@@ -1136,6 +1137,7 @@ def check_time_limit_for_change_all_propagate_mode(
         ).values_list("message_id", flat=True)
         messages_allowed_to_move: List[int] = list(
             Message.objects.filter(
+                # Uses index: zerver_message_pkey
                 id__in=accessible_messages_in_topic,
                 date_sent__gt=timezone_now()
                 - datetime.timedelta(seconds=message_move_deadline_seconds),
@@ -1146,7 +1148,7 @@ def check_time_limit_for_change_all_propagate_mode(
         total_messages_requested_to_move = len(accessible_messages_in_topic)
     else:
         all_messages_in_topic = (
-            messages_for_topic(message.recipient_id, message.topic_name())
+            messages_for_topic(message.realm_id, message.recipient_id, message.topic_name())
             .order_by("id")
             .values_list("id", "date_sent")
         )
diff --git a/zerver/actions/message_flags.py b/zerver/actions/message_flags.py
index f10f86c1f6..1b4da063bf 100644
--- a/zerver/actions/message_flags.py
+++ b/zerver/actions/message_flags.py
@@ -276,6 +276,7 @@ def do_update_message_flags(
             subscribed_recipient_ids = get_subscribed_stream_recipient_ids_for_user(user_profile)
 
             message_ids_in_unsubscribed_streams = set(
+                # Uses index: zerver_message_pkey
                 Message.objects.select_related("recipient")
                 .filter(id__in=messages, recipient__type=Recipient.STREAM)
                 .exclude(recipient_id__in=subscribed_recipient_ids)
@@ -326,6 +327,7 @@ def do_update_message_flags(
             historical_messages = bulk_access_messages(
                 user_profile,
                 list(
+                    # Uses index: zerver_message_pkey
                     Message.objects.filter(id__in=historical_message_ids).prefetch_related(
                         "recipient"
                     )
diff --git a/zerver/actions/message_send.py b/zerver/actions/message_send.py
index c25ac74d8e..efb2ec4d19 100644
--- a/zerver/actions/message_send.py
+++ b/zerver/actions/message_send.py
@@ -232,7 +232,7 @@ def get_recipient_info(
             # has syntax that might be a @topic mention without having confirmed the syntax isn't, say,
             # in a code block.
             topic_participant_user_ids = participants_for_topic(
-                recipient.id, stream_topic.topic_name
+                realm_id, recipient.id, stream_topic.topic_name
             )
         subscription_rows = (
             get_subscriptions_for_send_message(
@@ -1085,6 +1085,8 @@ def already_sent_mirrored_message_id(message: Message) -> Optional[int]:
         time_window = datetime.timedelta(seconds=0)
 
     messages = Message.objects.filter(
+        # Uses index: zerver_message_realm_recipient_subject
+        realm_id=message.realm_id,
         sender=message.sender,
         recipient=message.recipient,
         subject=message.topic_name(),
diff --git a/zerver/actions/realm_settings.py b/zerver/actions/realm_settings.py
index 620432754f..ec453339c6 100644
--- a/zerver/actions/realm_settings.py
+++ b/zerver/actions/realm_settings.py
@@ -420,8 +420,11 @@ def do_scrub_realm(realm: Realm, *, acting_user: Optional[UserProfile]) -> None:
     )
     cross_realm_bot_message_ids = list(
         Message.objects.filter(
-            # Filtering by both message.recipient and message.realm is more robust for ensuring
-            # no messages belonging to another realm will be deleted due to some bugs.
+            # Filtering by both message.recipient and message.realm is
+            # more robust for ensuring no messages belonging to
+            # another realm will be deleted due to some bugs.
+            #
+            # Uses index: zerver_message_realm_sender_recipient
             sender__realm=internal_realm,
             recipient_id__in=all_recipient_ids_in_realm,
             realm=realm,
diff --git a/zerver/actions/streams.py b/zerver/actions/streams.py
index e205e2b493..8ccf1c16ea 100644
--- a/zerver/actions/streams.py
+++ b/zerver/actions/streams.py
@@ -193,7 +193,11 @@ def do_reactivate_stream(
 
     # Update caches
     cache_set(display_recipient_cache_key(stream.recipient_id), new_name)
-    messages = Message.objects.filter(recipient_id=stream.recipient_id).only("id")
+    messages = Message.objects.filter(
+        # Uses index: zerver_message_realm_recipient_id
+        realm_id=realm.id,
+        recipient_id=stream.recipient_id,
+    ).only("id")
     cache_delete_many(to_dict_cache_key_id(message.id) for message in messages)
 
     # Unset the is_web_public cache on attachments, since the stream is now private.
@@ -284,11 +288,17 @@ def merge_streams(
     # this before removing the subscription objects, to avoid messages
     # "disappearing" if an error interrupts this function.
     message_ids_to_clear = list(
-        Message.objects.filter(recipient=recipient_to_destroy).values_list("id", flat=True)
-    )
-    count = Message.objects.filter(recipient=recipient_to_destroy).update(
-        recipient=recipient_to_keep
+        Message.objects.filter(
+            # Uses index: zerver_message_realm_recipient_id
+            realm_id=realm.id,
+            recipient=recipient_to_destroy,
+        ).values_list("id", flat=True)
     )
+    count = Message.objects.filter(
+        # Uses index: zerver_message_realm_recipient_id (prefix)
+        realm_id=realm.id,
+        recipient=recipient_to_destroy,
+    ).update(recipient=recipient_to_keep)
     bulk_delete_cache_keys(message_ids_to_clear)
 
     # Remove subscriptions to the old stream.
@@ -1185,7 +1195,11 @@ def do_rename_stream(stream: Stream, new_name: str, user_profile: UserProfile) -
 
     assert stream.recipient_id is not None
     recipient_id: int = stream.recipient_id
-    messages = Message.objects.filter(recipient_id=recipient_id).only("id")
+    messages = Message.objects.filter(
+        # Uses index: zerver_message_realm_recipient_id
+        realm_id=stream.realm_id,
+        recipient_id=recipient_id,
+    ).only("id")
 
     cache_set(display_recipient_cache_key(recipient_id), stream.name)
 
diff --git a/zerver/actions/users.py b/zerver/actions/users.py
index 750f16dafe..1fe2a703ff 100644
--- a/zerver/actions/users.py
+++ b/zerver/actions/users.py
@@ -189,7 +189,10 @@ def do_delete_user_preserving_messages(user_profile: UserProfile) -> None:
             force_date_joined=date_joined,
             create_personal_recipient=False,
         )
-        Message.objects.filter(sender=user_profile).update(sender=temp_replacement_user)
+        # Uses index: zerver_message_realm_sender_recipient (prefix)
+        Message.objects.filter(realm_id=realm.id, sender=user_profile).update(
+            sender=temp_replacement_user
+        )
         Subscription.objects.filter(
             user_profile=user_profile, recipient__type=Recipient.HUDDLE
         ).update(user_profile=temp_replacement_user)
@@ -212,7 +215,10 @@ def do_delete_user_preserving_messages(user_profile: UserProfile) -> None:
         replacement_user.recipient = personal_recipient
         replacement_user.save(update_fields=["recipient"])
 
-        Message.objects.filter(sender=temp_replacement_user).update(sender=replacement_user)
+        # Uses index: zerver_message_realm_sender_recipient (prefix)
+        Message.objects.filter(realm_id=realm.id, sender=temp_replacement_user).update(
+            sender=replacement_user
+        )
         Subscription.objects.filter(
             user_profile=temp_replacement_user, recipient__type=Recipient.HUDDLE
         ).update(user_profile=replacement_user, is_user_active=replacement_user.is_active)
diff --git a/zerver/lib/digest.py b/zerver/lib/digest.py
index 0c6a824c1c..e184947df3 100644
--- a/zerver/lib/digest.py
+++ b/zerver/lib/digest.py
@@ -162,6 +162,7 @@ def _enqueue_emails_for_realm(realm: Realm, cutoff: datetime.datetime) -> None:
 
 
 def get_recent_topics(
+    realm_id: int,
     stream_ids: List[int],
     cutoff_date: datetime.datetime,
 ) -> List[DigestTopic]:
@@ -171,7 +172,9 @@ def get_recent_topics(
     #   * number of senders
 
     messages = (
+        # Uses index: zerver_message_realm_recipient_date_sent
         Message.objects.filter(
+            realm_id=realm_id,
             recipient__type=Recipient.STREAM,
             recipient__type_id__in=stream_ids,
             date_sent__gt=cutoff_date,
@@ -307,7 +310,7 @@ def bulk_get_digest_context(
     # Get all the recent topics for all the users.  This does the heavy
     # lifting of making an expensive query to the Message table.  Then
     # for each user, we filter to just the streams they care about.
-    recent_topics = get_recent_topics(sorted(all_stream_ids), cutoff_date)
+    recent_topics = get_recent_topics(realm.id, sorted(all_stream_ids), cutoff_date)
 
     stream_map = get_slim_stream_map(all_stream_ids)
 
diff --git a/zerver/lib/email_notifications.py b/zerver/lib/email_notifications.py
index 1c05a7d753..d7d445ae5b 100644
--- a/zerver/lib/email_notifications.py
+++ b/zerver/lib/email_notifications.py
@@ -629,6 +629,7 @@ def handle_missedmessage_emails(
     # messages that were permanently deleted, since those would now be
     # in the ArchivedMessage table, not the Message table.
     messages = Message.objects.filter(
+        # Uses index: zerver_message_pkey
         usermessage__user_profile_id=user_profile,
         id__in=message_ids,
         usermessage__flags=~UserMessage.flags.read,
diff --git a/zerver/lib/export.py b/zerver/lib/export.py
index 509d63c473..c1d44189f5 100644
--- a/zerver/lib/export.py
+++ b/zerver/lib/export.py
@@ -1314,6 +1314,8 @@ def export_partial_message_files(
 
     if public_only:
         messages_we_received = Message.objects.filter(
+            # Uses index: zerver_message_realm_sender_recipient
+            realm_id=realm.id,
             sender__in=ids_of_our_possible_senders,
             recipient__in=recipient_ids_for_us,
         )
@@ -1329,6 +1331,8 @@ def export_partial_message_files(
         # anyone in the export and received by any of the users who we
         # have consent to export.
         messages_we_received = Message.objects.filter(
+            # Uses index: zerver_message_realm_sender_recipient
+            realm_id=realm.id,
             sender__in=ids_of_our_possible_senders,
             recipient__in=recipient_ids_for_us,
         )
@@ -1345,6 +1349,8 @@ def export_partial_message_files(
             messages_we_received_in_protected_history_streams = Message.objects.annotate(
                 has_usermessage=has_usermessage_expression
             ).filter(
+                # Uses index: zerver_message_realm_sender_recipient
+                realm_id=realm.id,
                 sender__in=ids_of_our_possible_senders,
                 recipient_id__in=(
                     set(consented_recipient_ids) & set(streams_with_protected_history_recipient_ids)
@@ -1370,6 +1376,8 @@ def export_partial_message_files(
         recipient_ids_for_them = get_ids(recipients_for_them)
 
         messages_we_sent_to_them = Message.objects.filter(
+            # Uses index: zerver_message_realm_sender_recipient
+            realm_id=realm.id,
             sender__in=consented_user_ids,
             recipient__in=recipient_ids_for_them,
         )
@@ -1410,6 +1418,7 @@ def write_message_partials(
     dump_file_id = 1
 
     for message_id_chunk in message_id_chunks:
+        # Uses index: zerver_message_pkey
         actual_query = Message.objects.filter(id__in=message_id_chunk).order_by("id")
         message_chunk = make_raw(actual_query)
 
@@ -2253,13 +2262,21 @@ def export_messages_single_user(
 
         return ", ".join(user_names)
 
-    messages_from_me = Message.objects.filter(sender=user_profile)
+    messages_from_me = Message.objects.filter(
+        # Uses index: zerver_message_realm_sender_recipient (prefix)
+        realm_id=user_profile.realm_id,
+        sender=user_profile,
+    )
 
     my_subscriptions = Subscription.objects.filter(
         user_profile=user_profile, recipient__type__in=[Recipient.PERSONAL, Recipient.HUDDLE]
     )
     my_recipient_ids = [sub.recipient_id for sub in my_subscriptions]
-    messages_to_me = Message.objects.filter(recipient_id__in=my_recipient_ids)
+    messages_to_me = Message.objects.filter(
+        # Uses index: zerver_message_realm_recipient_id (prefix)
+        realm_id=user_profile.realm_id,
+        recipient_id__in=my_recipient_ids,
+    )
 
     # Find all message ids that pertain to us.
     all_message_ids: Set[int] = set()
diff --git a/zerver/lib/home.py b/zerver/lib/home.py
index 86de33e8db..eb1741bf41 100644
--- a/zerver/lib/home.py
+++ b/zerver/lib/home.py
@@ -228,7 +228,13 @@ def build_page_params_for_home_page_load(
         # In narrow_stream context, initial pointer is just latest message
         recipient = narrow_stream.recipient
         page_params["max_message_id"] = -1
-        max_message = Message.objects.filter(recipient=recipient).order_by("-id").only("id").first()
+        max_message = (
+            # Uses index: zerver_message_realm_recipient_id
+            Message.objects.filter(realm_id=realm.id, recipient=recipient)
+            .order_by("-id")
+            .only("id")
+            .first()
+        )
         if max_message:
             page_params["max_message_id"] = max_message.id
         page_params["narrow_stream"] = narrow_stream.name
diff --git a/zerver/lib/message.py b/zerver/lib/message.py
index 5e049d290c..0d2286257a 100644
--- a/zerver/lib/message.py
+++ b/zerver/lib/message.py
@@ -511,6 +511,7 @@ class MessageDict:
             "sending_client__name",
             "sender__realm_id",
         ]
+        # Uses index: zerver_message_pkey
         messages = Message.objects.filter(id__in=needed_ids).values(*fields)
         return MessageDict.sew_submessages_and_reactions_to_msgs(messages)
 
@@ -1476,6 +1477,7 @@ def update_first_visible_message_id(realm: Realm) -> None:
     else:
         try:
             first_visible_message_id = (
+                # Uses index: zerver_message_realm_id
                 Message.objects.filter(realm=realm)
                 .values("id")
                 .order_by("-id")[realm.message_visibility_limit - 1]["id"]
diff --git a/zerver/lib/retention.py b/zerver/lib/retention.py
index 1510aef7ce..2156c36446 100644
--- a/zerver/lib/retention.py
+++ b/zerver/lib/retention.py
@@ -189,12 +189,14 @@ def move_expired_messages_to_archive_by_recipient(
 ) -> int:
     assert message_retention_days != -1
 
+    # Uses index: zerver_message_realm_recipient_date_sent
     query = SQL(
         """
     INSERT INTO zerver_archivedmessage ({dst_fields}, archive_transaction_id)
         SELECT {src_fields}, {archive_transaction_id}
         FROM zerver_message
-        WHERE zerver_message.recipient_id = {recipient_id}
+        WHERE zerver_message.realm_id = {realm_id}
+            AND zerver_message.recipient_id = {recipient_id}
             AND zerver_message.date_sent < {check_date}
         LIMIT {chunk_size}
     ON CONFLICT (id) DO UPDATE SET archive_transaction_id = {archive_transaction_id}
@@ -207,6 +209,7 @@ def move_expired_messages_to_archive_by_recipient(
         query,
         type=ArchiveTransaction.RETENTION_POLICY_BASED,
         realm=realm,
+        realm_id=Literal(realm.id),
         recipient_id=Literal(recipient.id),
         check_date=Literal(check_date.isoformat()),
         chunk_size=chunk_size,
@@ -224,6 +227,7 @@ def move_expired_personal_and_huddle_messages_to_archive(
     recipient_types = (Recipient.PERSONAL, Recipient.HUDDLE)
 
     # Archive expired personal and huddle Messages in the realm, including cross-realm messages.
+    # Uses index: zerver_message_realm_recipient_date_sent
     query = SQL(
         """
     INSERT INTO zerver_archivedmessage ({dst_fields}, archive_transaction_id)
@@ -318,6 +322,8 @@ def delete_messages(msg_ids: List[int]) -> None:
     # key to Message (due to `on_delete=CASCADE` in our models
     # configuration), so we need to be sure we've taken care of
     # archiving the messages before doing this step.
+    #
+    # Uses index: zerver_message_pkey
     Message.objects.filter(id__in=msg_ids).delete()
 
 
@@ -453,6 +459,7 @@ def get_realms_and_streams_for_archiving() -> List[Tuple[Realm, List[Stream]]]:
 def move_messages_to_archive(
     message_ids: List[int], realm: Optional[Realm] = None, chunk_size: int = MESSAGE_BATCH_SIZE
 ) -> None:
+    # Uses index: zerver_message_pkey
     query = SQL(
         """
     INSERT INTO zerver_archivedmessage ({dst_fields}, archive_transaction_id)
diff --git a/zerver/lib/scheduled_messages.py b/zerver/lib/scheduled_messages.py
index 1cba74856c..39fbc625c8 100644
--- a/zerver/lib/scheduled_messages.py
+++ b/zerver/lib/scheduled_messages.py
@@ -24,6 +24,7 @@ def get_undelivered_scheduled_messages(
     user_profile: UserProfile,
 ) -> List[Union[APIScheduledDirectMessageDict, APIScheduledStreamMessageDict]]:
     scheduled_messages = ScheduledMessage.objects.filter(
+        realm_id=user_profile.realm_id,
         sender=user_profile,
         # Notably, we don't require failed=False, since we will want
         # to display those to users.
diff --git a/zerver/lib/soft_deactivation.py b/zerver/lib/soft_deactivation.py
index f1eee37f42..7a25f8f3c4 100644
--- a/zerver/lib/soft_deactivation.py
+++ b/zerver/lib/soft_deactivation.py
@@ -210,7 +210,10 @@ def add_missing_messages(user_profile: UserProfile) -> None:
 
     all_stream_msgs = list(
         Message.objects.filter(
-            recipient_id__in=recipient_ids, id__gt=user_profile.last_active_message_id
+            # Uses index: zerver_message_realm_recipient_id
+            realm_id=user_profile.realm_id,
+            recipient_id__in=recipient_ids,
+            id__gt=user_profile.last_active_message_id,
         )
         .order_by("id")
         .values("id", "recipient__type_id")
diff --git a/zerver/lib/topic.py b/zerver/lib/topic.py
index a2353a63ed..66e6675858 100644
--- a/zerver/lib/topic.py
+++ b/zerver/lib/topic.py
@@ -92,8 +92,12 @@ def filter_by_topic_name_via_message(
     return query.filter(message__subject__iexact=topic_name)
 
 
-def messages_for_topic(stream_recipient_id: int, topic_name: str) -> QuerySet[Message]:
+def messages_for_topic(
+    realm_id: int, stream_recipient_id: int, topic_name: str
+) -> QuerySet[Message]:
     return Message.objects.filter(
+        # Uses index: zerver_message_realm_recipient_upper_subject
+        realm_id=realm_id,
         recipient_id=stream_recipient_id,
         subject__iexact=topic_name,
     )
@@ -149,13 +153,17 @@ def update_messages_for_topic_edit(
     edit_history_event: EditHistoryEvent,
     last_edit_time: datetime,
 ) -> List[Message]:
-    propagate_query = Q(recipient_id=old_stream.recipient_id, subject__iexact=orig_topic_name)
+    propagate_query = Q(
+        recipient_id=old_stream.recipient_id,
+        subject__iexact=orig_topic_name,
+    )
     if propagate_mode == "change_all":
         propagate_query = propagate_query & ~Q(id=edited_message.id)
     if propagate_mode == "change_later":
         propagate_query = propagate_query & Q(id__gt=edited_message.id)
 
-    messages = Message.objects.filter(propagate_query).select_related(
+    # Uses index: zerver_message_realm_recipient_upper_subject
+    messages = Message.objects.filter(propagate_query, realm_id=old_stream.realm_id).select_related(
         *Message.DEFAULT_SELECT_RELATED
     )
 
@@ -283,12 +291,17 @@ def get_topic_resolution_and_bare_name(stored_name: str) -> Tuple[bool, str]:
     return (False, stored_name)
 
 
-def participants_for_topic(recipient_id: int, topic_name: str) -> Set[int]:
+def participants_for_topic(realm_id: int, recipient_id: int, topic_name: str) -> Set[int]:
     """
     Users who either sent or reacted to the messages in the topic.
     The function is expensive for large numbers of messages in the topic.
     """
-    messages = Message.objects.filter(recipient_id=recipient_id, subject__iexact=topic_name)
+    messages = Message.objects.filter(
+        # Uses index: zerver_message_realm_recipient_upper_subject
+        realm_id=realm_id,
+        recipient_id=recipient_id,
+        subject__iexact=topic_name,
+    )
     participants = set(
         UserProfile.objects.filter(
             Q(id__in=Subquery(messages.values("sender_id")))
diff --git a/zerver/models.py b/zerver/models.py
index 4045be6a4b..27a15d4c43 100644
--- a/zerver/models.py
+++ b/zerver/models.py
@@ -3189,6 +3189,8 @@ class Message(AbstractMessage):
 
 def get_context_for_message(message: Message) -> QuerySet[Message]:
     return Message.objects.filter(
+        # Uses index: zerver_message_realm_recipient_upper_subject
+        realm_id=message.realm_id,
         recipient_id=message.recipient_id,
         subject__iexact=message.subject,
         id__lt=message.id,
@@ -3676,6 +3678,8 @@ def validate_attachment_request_for_spectator_access(
         Attachment.objects.filter(id=attachment.id, is_web_public__isnull=True).update(
             is_web_public=Exists(
                 Message.objects.filter(
+                    # Uses index: zerver_attachment_messages_attachment_id_message_id_key
+                    realm_id=realm.id,
                     attachment=OuterRef("id"),
                     recipient__stream__invite_only=False,
                     recipient__stream__is_web_public=True,
@@ -3723,6 +3727,8 @@ def validate_attachment_request(
         Attachment.objects.filter(id=attachment.id, is_realm_public__isnull=True).update(
             is_realm_public=Exists(
                 Message.objects.filter(
+                    # Uses index: zerver_attachment_messages_attachment_id_message_id_key
+                    realm_id=user_profile.realm_id,
                     attachment=OuterRef("id"),
                     recipient__stream__invite_only=False,
                 ),
diff --git a/zerver/tests/test_gitter_importer.py b/zerver/tests/test_gitter_importer.py
index e09f997617..cdb4c2ed6a 100644
--- a/zerver/tests/test_gitter_importer.py
+++ b/zerver/tests/test_gitter_importer.py
@@ -131,7 +131,7 @@ class GitterImporter(ZulipTestCase):
 
         # test rendered_messages
         realm_users = UserProfile.objects.filter(realm=realm)
-        messages = Message.objects.filter(sender__in=realm_users)
+        messages = Message.objects.filter(realm_id=realm.id, sender__in=realm_users)
         for message in messages:
             self.assertIsNotNone(message.rendered_content, None)
 
diff --git a/zerver/tests/test_import_export.py b/zerver/tests/test_import_export.py
index e82dc074ca..9ae63c0df8 100644
--- a/zerver/tests/test_import_export.py
+++ b/zerver/tests/test_import_export.py
@@ -643,7 +643,7 @@ class RealmImportExportTest(ExportFile):
             type_id__in=public_stream_ids, type=Recipient.STREAM
         )
         public_stream_message_ids = Message.objects.filter(
-            recipient__in=public_stream_recipients
+            realm_id=realm.id, recipient__in=public_stream_recipients
         ).values_list("id", flat=True)
 
         # Messages from Private stream C are not exported since no member gave consent
@@ -656,7 +656,7 @@ class RealmImportExportTest(ExportFile):
             type_id__in=private_stream_ids, type=Recipient.STREAM
         )
         private_stream_message_ids = Message.objects.filter(
-            recipient__in=private_stream_recipients
+            realm_id=realm.id, recipient__in=private_stream_recipients
         ).values_list("id", flat=True)
 
         pm_recipients = Recipient.objects.filter(
@@ -664,7 +664,7 @@ class RealmImportExportTest(ExportFile):
         )
         pm_query = Q(recipient__in=pm_recipients) | Q(sender__in=consented_user_ids)
         exported_pm_ids = (
-            Message.objects.filter(pm_query)
+            Message.objects.filter(pm_query, realm=realm.id)
             .values_list("id", flat=True)
             .values_list("id", flat=True)
         )
@@ -676,7 +676,7 @@ class RealmImportExportTest(ExportFile):
         )
         pm_query = Q(recipient__in=huddle_recipients) | Q(sender__in=consented_user_ids)
         exported_huddle_ids = (
-            Message.objects.filter(pm_query)
+            Message.objects.filter(pm_query, realm=realm.id)
             .values_list("id", flat=True)
             .values_list("id", flat=True)
         )
@@ -1260,7 +1260,7 @@ class RealmImportExportTest(ExportFile):
         # test messages
         def get_stream_messages(r: Realm) -> QuerySet[Message]:
             recipient = get_recipient_stream(r)
-            messages = Message.objects.filter(recipient=recipient)
+            messages = Message.objects.filter(realm_id=r.id, recipient=recipient)
             return messages
 
         @getter
diff --git a/zerver/tests/test_message_fetch.py b/zerver/tests/test_message_fetch.py
index bd4e8adf42..78aac7dcdb 100644
--- a/zerver/tests/test_message_fetch.py
+++ b/zerver/tests/test_message_fetch.py
@@ -2289,7 +2289,7 @@ class GetOldMessagesTest(ZulipTestCase):
         stream_names = ["Scotland", "Verona", "Venice"]
 
         def send_messages_to_all_streams() -> None:
-            Message.objects.filter(recipient__type=Recipient.STREAM).delete()
+            Message.objects.filter(realm_id=realm.id, recipient__type=Recipient.STREAM).delete()
             for stream_name in stream_names:
                 self.subscribe(hamlet, stream_name)
                 for i in range(num_messages_per_stream):
diff --git a/zerver/tests/test_realm.py b/zerver/tests/test_realm.py
index 5ebc2eecf2..75ffe83966 100644
--- a/zerver/tests/test_realm.py
+++ b/zerver/tests/test_realm.py
@@ -1573,9 +1573,24 @@ class ScrubRealmTest(ZulipTestCase):
 
         CustomProfileField.objects.create(realm=lear)
 
-        self.assertEqual(Message.objects.filter(sender__in=[iago, othello]).count(), 10)
-        self.assertEqual(Message.objects.filter(sender__in=[cordelia, king]).count(), 10)
-        self.assertEqual(Message.objects.filter(sender=notification_bot).count(), 6)
+        self.assertEqual(
+            Message.objects.filter(
+                realm_id__in=(zulip.id, lear.id), sender__in=[iago, othello]
+            ).count(),
+            10,
+        )
+        self.assertEqual(
+            Message.objects.filter(
+                realm_id__in=(zulip.id, lear.id), sender__in=[cordelia, king]
+            ).count(),
+            10,
+        )
+        self.assertEqual(
+            Message.objects.filter(
+                realm_id__in=(zulip.id, lear.id), sender=notification_bot
+            ).count(),
+            6,
+        )
         self.assertEqual(UserMessage.objects.filter(user_profile__in=[iago, othello]).count(), 25)
         self.assertEqual(UserMessage.objects.filter(user_profile__in=[cordelia, king]).count(), 25)
 
@@ -1584,9 +1599,24 @@ class ScrubRealmTest(ZulipTestCase):
         with self.assertLogs(level="WARNING"):
             do_scrub_realm(zulip, acting_user=None)
 
-        self.assertEqual(Message.objects.filter(sender__in=[iago, othello]).count(), 0)
-        self.assertEqual(Message.objects.filter(sender__in=[cordelia, king]).count(), 10)
-        self.assertEqual(Message.objects.filter(sender=notification_bot).count(), 3)
+        self.assertEqual(
+            Message.objects.filter(
+                realm_id__in=(zulip.id, lear.id), sender__in=[iago, othello]
+            ).count(),
+            0,
+        )
+        self.assertEqual(
+            Message.objects.filter(
+                realm_id__in=(zulip.id, lear.id), sender__in=[cordelia, king]
+            ).count(),
+            10,
+        )
+        self.assertEqual(
+            Message.objects.filter(
+                realm_id__in=(zulip.id, lear.id), sender=notification_bot
+            ).count(),
+            3,
+        )
         self.assertEqual(UserMessage.objects.filter(user_profile__in=[iago, othello]).count(), 0)
         self.assertEqual(UserMessage.objects.filter(user_profile__in=[cordelia, king]).count(), 25)
 
diff --git a/zerver/tests/test_retention.py b/zerver/tests/test_retention.py
index 74a3767330..8f6d7b61e8 100644
--- a/zerver/tests/test_retention.py
+++ b/zerver/tests/test_retention.py
@@ -697,7 +697,9 @@ class MoveMessageToArchiveGeneral(MoveMessageToArchiveBase):
         )
         for attachment_id in attachment_ids:
             attachment_id_to_message_ids[attachment_id] = list(
-                Message.objects.filter(attachment__id=attachment_id).values_list("id", flat=True),
+                Message.objects.filter(realm_id=realm_id, attachment__id=attachment_id).values_list(
+                    "id", flat=True
+                ),
             )
 
         usermsg_ids = self._get_usermessage_ids(msg_ids)
@@ -736,9 +738,9 @@ class MoveMessageToArchiveGeneral(MoveMessageToArchiveBase):
             self.assertEqual(
                 set(attachment_id_to_message_ids[attachment_id]),
                 set(
-                    Message.objects.filter(attachment__id=attachment_id).values_list(
-                        "id", flat=True
-                    )
+                    Message.objects.filter(
+                        realm_id=realm_id, attachment__id=attachment_id
+                    ).values_list("id", flat=True)
                 ),
             )
 
diff --git a/zerver/tests/test_signup.py b/zerver/tests/test_signup.py
index 0aeb94665c..0c9cc12b12 100644
--- a/zerver/tests/test_signup.py
+++ b/zerver/tests/test_signup.py
@@ -1306,13 +1306,17 @@ class RealmCreationTest(ZulipTestCase):
         ]:
             stream = get_stream(stream_name, realm)
             recipient = stream.recipient
-            messages = Message.objects.filter(recipient=recipient).order_by("date_sent")
+            messages = Message.objects.filter(realm_id=realm.id, recipient=recipient).order_by(
+                "date_sent"
+            )
             self.assert_length(messages, message_count)
             self.assertIn(text, messages[0].content)
 
         # Check admin organization's signups stream messages
         recipient = signups_stream.recipient
-        messages = Message.objects.filter(recipient=recipient).order_by("id")
+        messages = Message.objects.filter(realm_id=internal_realm.id, recipient=recipient).order_by(
+            "id"
+        )
         self.assert_length(messages, 1)
         # Check organization name, subdomain and organization type are in message content
         self.assertIn("Zulip Test", messages[0].content)
@@ -1610,7 +1614,9 @@ class RealmCreationTest(ZulipTestCase):
 
         # Make sure the correct Welcome Bot direct message is sent.
         welcome_msg = Message.objects.filter(
-            sender__email="welcome-bot@zulip.com", recipient__type=Recipient.PERSONAL
+            realm_id=get_realm(string_id).id,
+            sender__email="welcome-bot@zulip.com",
+            recipient__type=Recipient.PERSONAL,
         ).latest("id")
         self.assertTrue(welcome_msg.content.startswith("Hello, and welcome to Zulip!"))
 
@@ -1661,7 +1667,9 @@ class RealmCreationTest(ZulipTestCase):
 
         # Make sure the correct Welcome Bot direct message is sent.
         welcome_msg = Message.objects.filter(
-            sender__email="welcome-bot@zulip.com", recipient__type=Recipient.PERSONAL
+            realm_id=get_realm(string_id).id,
+            sender__email="welcome-bot@zulip.com",
+            recipient__type=Recipient.PERSONAL,
         ).latest("id")
         self.assertTrue(welcome_msg.content.startswith("Hello, and welcome to Zulip!"))
 
diff --git a/zerver/tests/test_users.py b/zerver/tests/test_users.py
index d015ab52c9..c5a6b38d03 100644
--- a/zerver/tests/test_users.py
+++ b/zerver/tests/test_users.py
@@ -2499,10 +2499,10 @@ class DeleteUserTest(ZulipTestCase):
         self.send_personal_message(hamlet, cordelia)
 
         personal_message_ids_to_hamlet = Message.objects.filter(
-            recipient=hamlet_personal_recipient
+            realm_id=realm.id, recipient=hamlet_personal_recipient
         ).values_list("id", flat=True)
         self.assertGreater(len(personal_message_ids_to_hamlet), 0)
-        self.assertTrue(Message.objects.filter(sender=hamlet).exists())
+        self.assertTrue(Message.objects.filter(realm_id=realm.id, sender=hamlet).exists())
 
         huddle_message_ids_from_cordelia = [
             self.send_huddle_message(cordelia, [hamlet, othello]) for i in range(3)
@@ -2535,7 +2535,9 @@ class DeleteUserTest(ZulipTestCase):
         self.assertEqual(Message.objects.filter(id__in=huddle_message_ids_from_hamlet).count(), 0)
         self.assertEqual(Message.objects.filter(id__in=huddle_message_ids_from_cordelia).count(), 3)
 
-        self.assertEqual(Message.objects.filter(sender_id=hamlet_user_id).count(), 0)
+        self.assertEqual(
+            Message.objects.filter(realm_id=realm.id, sender_id=hamlet_user_id).count(), 0
+        )
 
         # Verify that the dummy user is subscribed to the deleted user's huddles, to keep huddle data
         # in a correct state.
@@ -2564,10 +2566,10 @@ class DeleteUserTest(ZulipTestCase):
         self.send_personal_message(hamlet, cordelia)
 
         personal_message_ids_to_hamlet = Message.objects.filter(
-            recipient=hamlet_personal_recipient
+            realm_id=realm.id, recipient=hamlet_personal_recipient
         ).values_list("id", flat=True)
         self.assertGreater(len(personal_message_ids_to_hamlet), 0)
-        self.assertTrue(Message.objects.filter(sender=hamlet).exists())
+        self.assertTrue(Message.objects.filter(realm_id=realm.id, sender=hamlet).exists())
 
         huddle_message_ids_from_cordelia = [
             self.send_huddle_message(cordelia, [hamlet, othello]) for i in range(3)
@@ -2584,7 +2586,7 @@ class DeleteUserTest(ZulipTestCase):
         self.assertGreater(len(huddle_with_hamlet_recipient_ids), 0)
 
         original_messages_from_hamlet_count = Message.objects.filter(
-            sender_id=hamlet_user_id
+            realm_id=realm.id, sender_id=hamlet_user_id
         ).count()
         self.assertGreater(original_messages_from_hamlet_count, 0)
 
@@ -2614,7 +2616,7 @@ class DeleteUserTest(ZulipTestCase):
         )
 
         self.assertEqual(
-            Message.objects.filter(sender_id=hamlet_user_id).count(),
+            Message.objects.filter(realm_id=realm.id, sender_id=hamlet_user_id).count(),
             original_messages_from_hamlet_count,
         )
 
diff --git a/zerver/views/streams.py b/zerver/views/streams.py
index c43d6cef99..5c0cf8dc08 100644
--- a/zerver/views/streams.py
+++ b/zerver/views/streams.py
@@ -923,7 +923,9 @@ def delete_in_topic(
 ) -> HttpResponse:
     stream, ignored_sub = access_stream_by_id(user_profile, stream_id)
 
-    messages = messages_for_topic(assert_is_not_none(stream.recipient_id), topic_name)
+    messages = messages_for_topic(
+        user_profile.realm_id, assert_is_not_none(stream.recipient_id), topic_name
+    )
     # Note: It would be better to use bulk_access_messages here, which is our core function
     # for obtaining the accessible messages - and it's good to use it wherever we can,
     # so that we have a central place to keep up to date with our security model for
diff --git a/zerver/worker/queue_processors.py b/zerver/worker/queue_processors.py
index 4aac565da2..170541b50f 100644
--- a/zerver/worker/queue_processors.py
+++ b/zerver/worker/queue_processors.py
@@ -97,6 +97,7 @@ from zerver.models import (
     Realm,
     RealmAuditLog,
     ScheduledMessageNotificationEmail,
+    Stream,
     UserMessage,
     UserProfile,
     filter_to_valid_prereg_users,
@@ -1013,12 +1014,15 @@ class DeferredWorker(QueueProcessingWorker):
                 "Marking messages as read for all users, stream_recipient_id %s",
                 event["stream_recipient_id"],
             )
+            stream = Stream.objects.get(recipient_id=event["stream_recipient_id"])
             # This event is generated by the stream deactivation code path.
             batch_size = 100
             offset = 0
             while True:
                 messages = Message.objects.filter(
-                    recipient_id=event["stream_recipient_id"]
+                    # Uses index: zerver_message_realm_recipient_id
+                    realm_id=stream.realm_id,
+                    recipient_id=event["stream_recipient_id"],
                 ).order_by("id")[offset : offset + batch_size]
 
                 with transaction.atomic(savepoint=False):