diff --git a/init.el b/init.el
index 3eadda0..05991ad 100644
--- a/init.el
+++ b/init.el
@@ -700,7 +700,8 @@ With given ARG, display files in `db/important-document-path’."
 ;; * Org
 
 (use-package db-org
-  :commands (db/verify-refile-target
+  :commands (db/check-special-org-files-in-agenda
+             db/verify-refile-target
              org-reset-checkbox-state-maybe
              db/find-parent-task
              db/ensure-running-clock
@@ -1124,7 +1125,10 @@ in the main agenda view."
             ;; opening them manually
             (mapc #'find-file-noselect org-agenda-files)
 
-            (add-hook 'org-agenda-mode-hook #'hl-line-mode 'append)))
+            (add-hook 'org-agenda-mode-hook #'hl-line-mode 'append)
+
+            (advice-add 'org-agenda
+                        :before #'db/check-special-org-files-in-agenda)))
 
 ;; Capturing
 
diff --git a/site-lisp/db-org.el b/site-lisp/db-org.el
index 54878c8..39872d9 100644
--- a/site-lisp/db-org.el
+++ b/site-lisp/db-org.el
@@ -11,6 +11,24 @@
 
 ;;; Agenda Customization
 
+(defun db/check-special-org-files-in-agenda (&rest args)
+  "Check whether the special org-mode files are part of `org-agenda-files', ignoring ARGS.
+The special org-mode files are `db/org-default-work-file',
+`db/org-default-home-file', `db/org-default-notes-files', and
+`db/org-default-refile-file'."
+  (declare (ignore args))
+  (require 'org)
+  (let ((agenda-files (mapcar #'file-truename (org-agenda-files t))))
+    (dolist (file '(db/org-default-home-file
+                    db/org-default-work-file
+                    db/org-default-notes-file
+                    db/org-default-refile-file))
+      (when (and (symbol-value file)
+                 (not (member (file-truename (symbol-value file))
+                              agenda-files)))
+        (warn "File %s is not part of `org-agenda-files'."
+              file)))))
+
 (defun db/org-agenda-list-deadlines (&optional match)
   ;; XXX org-agenda-later does not work, fix this
   "Prepare agenda view that only lists upcoming deadlines.