diff --git a/tools/Makefile.unix b/tools/Makefile.unix
index ce40ffc97e..e09d198fc4 100644
--- a/tools/Makefile.unix
+++ b/tools/Makefile.unix
@@ -580,8 +580,6 @@ clean: subdir_clean
 	$(call DELFILE, nuttx-export*.zip)
 	$(call DELDIR, nuttx-export*)
 	$(call DELFILE, nuttx_user*)
-	$(call DELFILE, .cproject)
-	$(call DELFILE, .project)
 	$(call DELDIR, staging)
 	$(call CLEAN)
 
diff --git a/tools/Makefile.win b/tools/Makefile.win
index 2936da500a..5c6955219e 100644
--- a/tools/Makefile.win
+++ b/tools/Makefile.win
@@ -563,8 +563,6 @@ clean: subdir_clean
 	$(call DELFILE, nuttx-export*)
 	$(call DELFILE, nuttx_user*)
 	$(call DELFILE, .gdbinit)
-	$(call DELFILE, .cproject)
-	$(call DELFILE, .project)
 	$(call DELDIR, staging)
 	$(call CLEAN)