diff --git a/Makefile b/Makefile
index cc7e550a1bd..671f92c77e8 100644
--- a/Makefile
+++ b/Makefile
@@ -95,6 +95,8 @@ cross-compile-build-tools:
 	$(Verb) if [ ! -f BuildTools/Makefile ]; then \
           $(MKDIR) BuildTools; \
 	  cd BuildTools ; \
+	  unset CFLAGS ; \
+	  unset CXXFLAGS ; \
 	  $(PROJ_SRC_DIR)/configure --build=$(BUILD_TRIPLE) \
 		--host=$(BUILD_TRIPLE) --target=$(BUILD_TRIPLE); \
 	  cd .. ; \