diff --git a/Makefile b/Makefile
index 8df4712b73cb..842e74c075fa 100644
--- a/Makefile
+++ b/Makefile
@@ -1925,7 +1925,7 @@ quiet_cmd_gen_compile_commands = GEN     $@
       cmd_gen_compile_commands = $(PYTHON3) $< -a $(AR) -o $@ $(filter-out $<, $(real-prereqs))
 
 $(extmod_prefix)compile_commands.json: scripts/clang-tools/gen_compile_commands.py \
-	$(if $(KBUILD_EXTMOD),,$(KBUILD_VMLINUX_OBJS) $(KBUILD_VMLINUX_LIBS)) \
+	$(if $(KBUILD_EXTMOD)$(KBUILD_MIXED_TREE),,$(KBUILD_VMLINUX_OBJS) $(KBUILD_VMLINUX_LIBS)) \
 	$(if $(CONFIG_MODULES), $(MODORDER)) FORCE
 	$(call if_changed,gen_compile_commands)