diff --git a/core/cli/packages.el b/core/cli/packages.el
index a6434e405..978cba488 100644
--- a/core/cli/packages.el
+++ b/core/cli/packages.el
@@ -627,7 +627,8 @@ If ELPA-P, include packages installed with package.el (M-x package-install)."
            (if (not regraft-repos-p)
                (ignore (print! (info "Skipping regrafting")))
              (doom--cli-packages-regraft-repos repos-to-regraft))
-           (when (require 'comp nil t)
+           (when (and (require 'comp nil t)
+                      (native-comp-available-p))
              (if (not eln-p)
                  (ignore (print! (info "Skipping native bytecode")))
                (doom--cli-packages-purge-eln))))))))