diff --git a/Makefile b/Makefile
index 45730f61f7..409b711e12 100644
--- a/Makefile
+++ b/Makefile
@@ -235,7 +235,10 @@ config.mk:
 else
 -include $(RARCH_OBJ:.o=.d)
 ifeq ($(HAVE_CONFIG_MK),)
-config.mk: configure qb/*
+# The Wayland protocol sources are generated by configure, so a tree
+# configured before a protocol was added has no way to make the new
+# object: ask for the reconfigure rather than fail on a missing file.
+config.mk: configure qb/* gfx/common/wayland/generate_wayland_protos.sh
 	@echo "config.mk is outdated or non-existing. Run ./configure again."
 	@exit 1
 endif