diff --git a/Makefile b/Makefile
index 8bf96ca230..7b7c00704f 100644
--- a/Makefile
+++ b/Makefile
@@ -210,11 +210,11 @@ menuconfig:
 endif
 
 $(NUTTX_SRC):
-	$(Q) (./Tools/check_submodules.sh)
+	$(Q) ($(PX4_BASE)/Tools/check_submodules.sh)
 
 .PHONY: checksubmodules
 checksubmodules:
-	$(Q) (./Tools/check_submodules.sh)
+	$(Q) ($(PX4_BASE)/Tools/check_submodules.sh)
 
 .PHONY: updatesubmodules
 updatesubmodules: