diff --git a/core/core-packages.el b/core/core-packages.el
index 035625d60..c8069d0aa 100644
--- a/core/core-packages.el
+++ b/core/core-packages.el
@@ -903,11 +903,12 @@ If RECOMPILE-P is non-nil, only recompile out-of-date files."
           (condition-case ex
               (let ((use-package-expand-minimally t))
                 (push (expand-file-name "init.el" doom-emacs-dir) compile-targets)
-                (dolist (target (cl-delete-duplicates (mapcar #'file-truename compile-targets) :test #'string=))
-                  (when (or (not recompile-p)
-                            (let ((elc-file (byte-compile-dest-file target)))
-                              (and (file-exists-p elc-file)
-                                   (file-newer-than-file-p target elc-file))))
+                (dolist (target (cl-delete-duplicates (mapcar #'file-truename compile-targets) :test #'equal))
+                  (when (and (not (string-match-p "/\\(packages\\|doctor\\)\\.el$" target))
+                             (or (not recompile-p)
+                                 (let ((elc-file (byte-compile-dest-file target)))
+                                   (and (file-exists-p elc-file)
+                                        (file-newer-than-file-p target elc-file)))))
                     (let ((result (if (doom-packages--read-if-cookies target)
                                       (byte-compile-file target)
                                     'no-byte-compile))