diff --git a/core/cli/env.el b/core/cli/env.el
index 1bb040d80..bc73c08c7 100644
--- a/core/cli/env.el
+++ b/core/cli/env.el
@@ -94,25 +94,6 @@ default, on Linux, this is '$SHELL -ic /usr/bin/env'. Variables in
                  "Generating")
                (relpath doom-env-file doom-emacs-dir))
       (let ((process-environment doom--initial-process-environment))
-        (insert
-         (concat
-          "# -*- mode: dotenv -*-\n"
-          (format "# Generated with: %s %s %s\n"
-                  shell-file-name
-                  doom-env-switches
-                  doom-env-executable)
-          "# ---------------------------------------------------------------------------\n"
-          "# This file was auto-generated by `doom env refresh'. It contains a list of\n"
-          "# environment variables scraped from your default shell (excluding variables\n"
-          "# blacklisted in doom-env-ignored-vars).\n"
-          "#\n"
-          "# It is NOT safe to edit this file. Changes will be overwritten next time that\n"
-          "# `doom env refresh` is executed. Alternatively, create your own env file and\n"
-          "# load it with `(doom-load-envvars-file FILE)`.\n"
-          "#\n"
-          "# To auto-regenerate this file when `doom reload` is run, use `doom env auto' or\n"
-          "# set DOOMENV=1 in your shell environment/config.\n"
-          "# ---------------------------------------------------------------------------\n\n"))
         (let ((shell-command-switch doom-env-switches)
               (error-buffer (get-buffer-create "*env errors*")))
           (print! (info "Scraping shell environment with '%s %s %s'")
@@ -138,6 +119,26 @@ default, on Linux, this is '$SHELL -ic /usr/bin/env'. Variables in
                                 return t)
                    (print! (info "Ignoring %s") var)
                    (delete-region (match-beginning 0) (1- valend)))))))
+          (goto-char (point-min))
+          (insert
+           (concat
+            "# -*- mode: dotenv -*-\n"
+            (format "# Generated with: %s %s %s\n"
+                    shell-file-name
+                    doom-env-switches
+                    doom-env-executable)
+            "# ---------------------------------------------------------------------------\n"
+            "# This file was auto-generated by `doom env refresh'. It contains a list of\n"
+            "# environment variables scraped from your default shell (excluding variables\n"
+            "# blacklisted in doom-env-ignored-vars).\n"
+            "#\n"
+            "# It is NOT safe to edit this file. Changes will be overwritten next time that\n"
+            "# `doom env refresh` is executed. Alternatively, create your own env file and\n"
+            "# load it with `(doom-load-envvars-file FILE)`.\n"
+            "#\n"
+            "# To auto-regenerate this file when `doom reload` is run, use `doom env auto' or\n"
+            "# set DOOMENV=1 in your shell environment/config.\n"
+            "# ---------------------------------------------------------------------------\n\n"))
           (print! (success "Successfully generated %S")
                   (relpath doom-env-file doom-emacs-dir))
           t)))))