diff --git a/Makefile b/Makefile
index 1f9e7f6fe8..d446302155 100644
--- a/Makefile
+++ b/Makefile
@@ -358,10 +358,10 @@ external-deps:
 #
 #############################################################
 clean: $(TARGETS_CLEAN)
-	rm -rf $(STAGING_DIR) $(TARGET_DIR) $(IMAGE)
+	rm -rf $(STAGING_DIR) $(TARGET_DIR) $(IMAGE) $(PROJECT_BUILD_DIR)/.root $(PROJECT_BUILD_DIR)/autotools-stamps
 
 dirclean: $(TARGETS_DIRCLEAN)
-	rm -rf $(STAGING_DIR) $(TARGET_DIR) $(IMAGE)
+	rm -rf $(STAGING_DIR) $(TARGET_DIR) $(IMAGE) $(PROJECT_BUILD_DIR)/.root $(PROJECT_BUILD_DIR)/autotools-stamps
 
 distclean:
 ifeq ($(DL_DIR),$(BASE_DIR)/dl)