diff --git a/mk/environ.mk b/mk/environ.mk
index bb4cbd6a59..6cc9434b43 100644
--- a/mk/environ.mk
+++ b/mk/environ.mk
@@ -120,6 +120,15 @@ ifneq ($(findstring CYGWIN, $(SYSTYPE)),)
   endif
 endif
 
+ifneq ($(findstring mavlink2, $(MAKECMDGOALS)),)
+EXTRAFLAGS += -DMAVLINK_PROTOCOL_VERSION=2
+MAVLINK_SUBDIR=v2.0
+MAVLINK_WIRE_PROTOCOL=2.0
+else
+MAVLINK_SUBDIR=v1.0
+MAVLINK_WIRE_PROTOCOL=1.0
+endif
+
 ifneq ($(APPDIR),)
 # this is a recusive PX4 build
 HAL_BOARD = HAL_BOARD_PX4
diff --git a/mk/mavgen.mk b/mk/mavgen.mk
index 4a43ea7ada..c51bad284f 100644
--- a/mk/mavgen.mk
+++ b/mk/mavgen.mk
@@ -2,11 +2,11 @@
 # mavlink header generation
 MAVLINK_DIR := $(SKETCHBOOK)/modules/mavlink/
 MESSAGE_DEFINITIONS := $(SKETCHBOOK)/modules/mavlink/message_definitions/v1.0
-MAVLINK_HEADERS := $(BUILDROOT)/libraries/GCS_MAVLink/include/mavlink/v1.0/ardupilotmega/mavlink.h $(wildcard $(BUILDROOT)/libraries/GCS_MAVLink/include/mavlink/v1.0/,*.h) $(wildcard $(BUILDROOT)/libraries/GCS_MAVLink/include/mavlink/v1.0/ardupilotmega,*.h)
-MAVLINK_OUTPUT_DIR := $(BUILDROOT)/libraries/GCS_MAVLink/include/mavlink/v1.0
+MAVLINK_HEADERS := $(BUILDROOT)/libraries/GCS_MAVLink/include/mavlink/$(MAVLINK_SUBDIR)/ardupilotmega/mavlink.h $(wildcard $(BUILDROOT)/libraries/GCS_MAVLink/include/mavlink/$(MAVLINK_SUBDIR)/,*.h) $(wildcard $(BUILDROOT)/libraries/GCS_MAVLink/include/mavlink/$(MAVLINK_SUBDIR)/ardupilotmega,*.h)
+MAVLINK_OUTPUT_DIR := $(BUILDROOT)/libraries/GCS_MAVLink/include/mavlink/$(MAVLINK_SUBDIR)
 
 $(MAVLINK_HEADERS): $(MESSAGE_DEFINITIONS)/ardupilotmega.xml $(MESSAGE_DEFINITIONS)/common.xml
 	echo "Generating MAVLink headers..."
 	#goto mavlink module directory and run the most recent generator script
 	echo "Generating C code using mavgen.py located at" $(SKETCHBOOK)/modules/mavlink/
-	-PYTHONPATH=$(MAVLINK_DIR) python $(MAVLINK_DIR)/pymavlink/tools/mavgen.py --lang=C --wire-protocol=1.0 --output=$(MAVLINK_OUTPUT_DIR) $(MAVLINK_DIR)/message_definitions/v1.0/ardupilotmega.xml
+	-PYTHONPATH=$(MAVLINK_DIR) python $(MAVLINK_DIR)/pymavlink/tools/mavgen.py --lang=C --wire-protocol=$(MAVLINK_WIRE_PROTOCOL) --output=$(MAVLINK_OUTPUT_DIR) $(MESSAGE_DEFINITIONS)/ardupilotmega.xml
diff --git a/mk/targets.mk b/mk/targets.mk
index 4089044988..fcf063e438 100644
--- a/mk/targets.mk
+++ b/mk/targets.mk
@@ -107,9 +107,6 @@ qurt: all
 # support debug build
 %-debug: OPTFLAGS = -g -O0
 
-# support mavlink2 builds
-%-mavlink2: EXTRAFLAGS += "-DMAVLINK_PROTOCOL_VERSION=2"
-
 # support address sanitiser
 %-asan: OPTFLAGS = -g -O0 -fsanitize=address -fno-omit-frame-pointer
 %-asan: LDFLAGS += -fsanitize=address