diff --git a/src/Makefile b/src/Makefile
index 8ac15083a73e2..dc6bb88363bee 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -412,9 +412,12 @@ libjulia-codegen-debug libjulia-codegen-release: $(PUBLIC_HEADER_TARGETS)
 
 clean:
 	-rm -fr $(build_shlibdir)/libjulia-internal* $(build_shlibdir)/libjulia-codegen* $(build_shlibdir)/libccalltest* $(build_shlibdir)/libllvmcalltest*
-	-rm -f $(BUILDDIR)/julia_flisp.boot $(BUILDDIR)/julia_flisp.boot.inc $(BUILDDIR)/jl_internal_funcs.inc
-	-rm -f $(BUILDDIR)/*.dbg.obj $(BUILDDIR)/*.o $(BUILDDIR)/*.dwo $(BUILDDIR)/*.$(SHLIB_EXT) $(BUILDDIR)/*.a $(BUILDDIR)/*.h.gen
+	-rm -f $(BUILDDIR)/julia_flisp.boot $(BUILDDIR)/julia_flisp.boot.inc
+	-rm -f $(BUILDDIR)/*.dbg.obj $(BUILDDIR)/*.o $(BUILDDIR)/*.dwo $(BUILDDIR)/*.$(SHLIB_EXT) $(BUILDDIR)/*.a
 	-rm -f $(BUILDDIR)/julia_version.h
+	# Cleanup generated headers, note we must also clean SRCDIR to avoid confusion in out-of-tree builds
+	-rm -f $(BUILDDIR)/jl_internal_funcs.inc $(BUILDDIR)/*.h.gen
+	-rm -f $(SRCDIR)/jl_internal_funcs.inc  $(SRCDIR)/*.h.gen
 
 clean-flisp:
 	-$(MAKE) -C $(SRCDIR)/flisp clean BUILDDIR='$(abspath $(BUILDDIR)/flisp)'