diff --git a/ports/zephyr/Makefile b/ports/zephyr/Makefile
index 2e6cb41b9..81aaaa6dc 100644
--- a/ports/zephyr/Makefile
+++ b/ports/zephyr/Makefile
@@ -90,7 +90,7 @@ build/genhdr/qstr.i.last: | $(Z_EXPORTS)
 LIBMICROPYTHON_EXTRA_CMD = -$(RM) -f outdir/$(OUTDIR_PREFIX)/zephyr.lnk
 
 # MicroPython's global clean cleans everything, fast
-CLEAN_EXTRA = outdir
+CLEAN_EXTRA = outdir prj_*_merged.conf
 
 # Clean Zephyr things in Zephyr way
 z_clean: