diff --git a/Makefile b/Makefile
index 9533e85a..f993f55e 100644
--- a/Makefile
+++ b/Makefile
@@ -1,6 +1,6 @@
 # Klipper build system
 #
-# Copyright (C) 2016  Kevin O'Connor <kevin@koconnor.net>
+# Copyright (C) 2016,2017  Kevin O'Connor <kevin@koconnor.net>
 #
 # This file may be distributed under the terms of the GNU GPLv3 license.
 
@@ -32,18 +32,16 @@ dirs-y = src
 cc-option=$(shell if test -z "`$(1) $(2) -S -o /dev/null -xc /dev/null 2>&1`" \
     ; then echo "$(2)"; else echo "$(3)"; fi ;)
 
-CFLAGS-y := -I$(OUT) -Isrc -I$(OUT)board-generic/ -O2 -MD -g \
+CFLAGS := -I$(OUT) -Isrc -I$(OUT)board-generic/ -O2 -MD -g \
     -Wall -Wold-style-definition $(call cc-option,$(CC),-Wtype-limits,) \
     -ffunction-sections -fdata-sections
-CFLAGS-y += -flto -fwhole-program -fno-use-linker-plugin
+CFLAGS += -flto -fwhole-program -fno-use-linker-plugin
 
-LDFLAGS-y := -Wl,--gc-sections -fno-whole-program
+CFLAGS_klipper.o = $(CFLAGS) -Wl,-r -nostdlib
+CFLAGS_klipper.elf = $(CFLAGS) -Wl,--gc-sections -fno-whole-program
 
 CPPFLAGS = -I$(OUT) -P -MD -MT $@
 
-CFLAGS = $(CFLAGS-y)
-LDFLAGS = $(LDFLAGS-y)
-
 # Default targets
 target-y := $(OUT)klipper.elf
 
@@ -83,7 +81,7 @@ $(OUT)declfunc.lds: src/declfunc.lds.S
 
 $(OUT)klipper.o: $(patsubst %.c, $(OUT)src/%.o,$(src-y)) $(OUT)declfunc.lds
 	@echo "  Linking $@"
-	$(Q)$(CC) $(CFLAGS) $(CFLAGS_klipper.o) -Wl,-r -Wl,-T,$(OUT)declfunc.lds -nostdlib $(patsubst %.c, $(OUT)src/%.o,$(src-y)) -o $@
+	$(Q)$(CC) $(CFLAGS_klipper.o) -Wl,-T,$(OUT)declfunc.lds $(patsubst %.c, $(OUT)src/%.o,$(src-y)) -o $@
 
 $(OUT)compile_time_request.o: $(OUT)klipper.o ./scripts/buildcommands.py
 	@echo "  Building $@"
@@ -93,7 +91,7 @@ $(OUT)compile_time_request.o: $(OUT)klipper.o ./scripts/buildcommands.py
 
 $(OUT)klipper.elf: $(OUT)klipper.o $(OUT)compile_time_request.o
 	@echo "  Linking $@"
-	$(Q)$(CC) $(CFLAGS) $(LDFLAGS) $^ -o $@
+	$(Q)$(CC) $(CFLAGS_klipper.elf) $^ -o $@
 
 ################ Kconfig rules
 
diff --git a/src/avr/Makefile b/src/avr/Makefile
index 444df365..fa9258b1 100644
--- a/src/avr/Makefile
+++ b/src/avr/Makefile
@@ -5,7 +5,7 @@ CROSS_PREFIX=avr-
 
 dirs-y += src/avr lib/pjrc_usb_serial
 
-CFLAGS-y += -mmcu=$(CONFIG_MCU)
+CFLAGS += -mmcu=$(CONFIG_MCU)
 
 # Add avr source files
 src-y += avr/main.c avr/timer.c avr/gpio.c
@@ -14,7 +14,7 @@ src-$(CONFIG_AVR_USBSERIAL) += avr/usbserial.c ../lib/pjrc_usb_serial/usb_serial
 src-$(CONFIG_AVR_SERIAL) += avr/serial.c
 
 # Suppress broken "misspelled signal handler" warnings on gcc 4.8.1
-CFLAGS_klipper.o := $(if $(filter 4.8.1, $(shell $(CC) -dumpversion)), -w)
+CFLAGS_klipper.o := $(CFLAGS_klipper.o) $(if $(filter 4.8.1, $(shell $(CC) -dumpversion)), -w)
 
 # Build the additional hex output file
 target-y += $(OUT)klipper.elf.hex
diff --git a/src/sam3x8e/Makefile b/src/sam3x8e/Makefile
index e3379630..5cf805e8 100644
--- a/src/sam3x8e/Makefile
+++ b/src/sam3x8e/Makefile
@@ -6,13 +6,13 @@ CROSS_PREFIX=arm-none-eabi-
 dirs-y += src/sam3x8e src/generic
 dirs-y += lib/cmsis-sam3x8e/source lib/cmsis-sam3x8e/source/gcc
 
-CFLAGS-y += -mthumb -mcpu=cortex-m3
-CFLAGS-y += -Ilib/cmsis-sam3x8e/include -Ilib/cmsis-sam3x8e/cmsis-include
-CFLAGS-y += -D__SAM3X8E__
+CFLAGS += -mthumb -mcpu=cortex-m3
+CFLAGS += -Ilib/cmsis-sam3x8e/include -Ilib/cmsis-sam3x8e/cmsis-include
+CFLAGS += -D__SAM3X8E__
 
-LDFLAGS-y += -Llib/cmsis-sam3x8e/source/gcc
-LDFLAGS-y += -T lib/cmsis-sam3x8e/source/gcc/sam3x8e_flash.ld
-LDFLAGS-y += --specs=nano.specs --specs=nosys.specs
+CFLAGS_klipper.elf += -Llib/cmsis-sam3x8e/source/gcc
+CFLAGS_klipper.elf += -T lib/cmsis-sam3x8e/source/gcc/sam3x8e_flash.ld
+CFLAGS_klipper.elf += --specs=nano.specs --specs=nosys.specs
 
 # Add source files
 src-y += sam3x8e/main.c sam3x8e/timer.c sam3x8e/gpio.c