diff --git a/modules/lang/emacs-lisp/config.el b/modules/lang/emacs-lisp/config.el
index c84354f5f..b9e3a8bce 100644
--- a/modules/lang/emacs-lisp/config.el
+++ b/modules/lang/emacs-lisp/config.el
@@ -56,7 +56,11 @@
   (defun +emacs-lisp|init-flycheck ()
     "Initialize flycheck-mode if not in emacs.d."
     (when (and buffer-file-name
-               (not (file-in-directory-p buffer-file-name doom-emacs-dir)))
+               (not (cl-loop for dir in (append (list doom-emacs-dir)
+                                                doom-modules-dirs
+                                                doom-psuedo-module-dirs)
+                             if (file-in-directory-p buffer-file-name dir)
+                             return t)))
       (flycheck-mode +1))))