--- a/Makefile
+++ b/Makefile
@@ -310,6 +310,7 @@ bootstrap-polyml:
 	$(RM) "$(BIN)/$(MLTON)"
 	$(MAKE) OLD_MLTON="$(BIN)/$(MLTON).polyml" all
 	$(RM) "$(LIB)/$(MLTON)-polyml$(EXE)"
+	$(RM) "$(LIB)/$(MLTON_OUTPUT)-polyml$(EXE)"
 	$(RM) "$(BIN)/$(MLTON).polyml"
 
 .PHONY: polyml-mlton
