diff --git a/mk/modules.mk b/mk/modules.mk
index 29d26d8fd5..4c40c65a06 100644
--- a/mk/modules.mk
+++ b/mk/modules.mk
@@ -1,11 +1,29 @@
 
 # git submodule support
 
+define echowarning
+@echo -e "\e[31mWARNING:\e[0m $1" >&2
+endef
+
+define echoallwarnings
+	$(call echowarning)
+	$(call echowarning)
+	$(call echowarning,make build system is deprecated for Linux boards)
+	$(call echowarning,new features are not going to be added anymore)
+	$(call echowarning,See README-WAF.md: https://github.com/ArduPilot/ardupilot/blob/master/README-WAF.md)
+	$(call echowarning)
+	$(call echowarning,The make build system will soon be removed)
+	$(call echowarning)
+	$(call echowarning)
+	@sleep 3
+endef
+
+CHECK_MODULES:
+	$(if $(BUILDSYS_DEPRECATED),$(call echoallwarnings))
+	$(v)$(MK_DIR)/check_modules.sh
+
 .PHONY: CHECK_MODULES
 all: CHECK_MODULES
 
-CHECK_MODULES:
-	$(v)$(MK_DIR)/check_modules.sh
-
 module-update:
 	git submodule update
diff --git a/mk/targets.mk b/mk/targets.mk
index 5fc6b202b7..f9a5bef9e4 100644
--- a/mk/targets.mk
+++ b/mk/targets.mk
@@ -20,10 +20,12 @@ flymaple-hil: flymaple
 
 linux: HAL_BOARD = HAL_BOARD_LINUX
 linux: TOOLCHAIN = NATIVE
+linux: BUILDSYS_DEPRECATED = 1
 linux: all
 
 erleboard: HAL_BOARD = HAL_BOARD_LINUX
 erleboard: TOOLCHAIN = BBONE
+erleboard: BUILDSYS_DEPRECATED = 1
 erleboard: all
 
 zynq: HAL_BOARD = HAL_BOARD_LINUX
@@ -34,41 +36,55 @@ zynq-hil : zynq
 
 pxf: HAL_BOARD = HAL_BOARD_LINUX
 pxf: TOOLCHAIN = BBONE
+pxf: BUILDSYS_DEPRECATED = 1
 pxf: all
 
 bebop: HAL_BOARD = HAL_BOARD_LINUX
 bebop: TOOLCHAIN = BBONE
 bebop: LDFLAGS += "-static"
+bebop: BUILDSYS_DEPRECATED = 1
 bebop: all
 
 minlure: HAL_BOARD = HAL_BOARD_LINUX
 minlure: TOOLCHAIN = NATIVE
+minlure: BUILDSYS_DEPRECATED = 1
 minlure: all
 
 navio: HAL_BOARD = HAL_BOARD_LINUX
 navio: TOOLCHAIN = RPI
+navio: BUILDSYS_DEPRECATED = 1
 navio: all
 
 navio2: HAL_BOARD = HAL_BOARD_LINUX
 navio2: TOOLCHAIN = RPI
+navio2: BUILDSYS_DEPRECATED = 1
 navio2: all
 
 raspilot: HAL_BOARD = HAL_BOARD_LINUX
 raspilot: TOOLCHAIN = RPI
+raspilot: BUILDSYS_DEPRECATED = 1
 raspilot: all
 
 erlebrain2: HAL_BOARD = HAL_BOARD_LINUX
 erlebrain2: TOOLCHAIN = RPI
+erlebrain2: BUILDSYS_DEPRECATED  = 1
 erlebrain2: all
 
 bbbmini: HAL_BOARD = HAL_BOARD_LINUX
 bbbmini: TOOLCHAIN = BBONE
+bbbmini: BUILDSYS_DEPRECATED  = 1
 bbbmini: all
 
 bhat: HAL_BOARD = HAL_BOARD_LINUX
 bhat: TOOLCHAIN = RPI
+bhat: BUILDSYS_DEPRECATED  = 1
 bhat: all
 
+pxfmini: HAL_BOARD = HAL_BOARD_LINUX
+pxfmini: TOOLCHAIN = RPI
+pxfmini: BUILDSYS_DEPRECATED  = 1
+pxfmini: all
+
 qflight: HAL_BOARD = HAL_BOARD_LINUX
 qflight: TOOLCHAIN = QFLIGHT
 qflight: all
@@ -81,10 +97,6 @@ qurt: HAL_BOARD = HAL_BOARD_QURT
 qurt: TOOLCHAIN = QURT
 qurt: all
 
-pxfmini: HAL_BOARD = HAL_BOARD_LINUX
-pxfmini: TOOLCHAIN = RPI
-pxfmini: all
-
 # cope with HIL targets
 %-hil: EXTRAFLAGS += "-DHIL_MODE=HIL_MODE_SENSORS "
 %-hilsensors: EXTRAFLAGS += "-DHIL_MODE=HIL_MODE_SENSORS "