diff --git a/core/autoload/config.el b/core/autoload/config.el
index 05637ad1e..6cb41fb0f 100644
--- a/core/autoload/config.el
+++ b/core/autoload/config.el
@@ -74,7 +74,9 @@ reloads your package list, and lastly, reloads your private config.el.
 Runs `doom-reload-hook' afterwards."
   (interactive)
   (require 'core-cli)
-  (doom--compile (format "%s refresh" doom-bin)
+  (when (and IS-WINDOWS (file-exists-p doom-env-file))
+    (warn "Can't regenerate envvar file from within Emacs. Run 'doom env' from the console"))
+  (doom--compile (format "%s refresh -e" doom-bin)
     :on-success
     (let ((doom-reloading-p t))
       (doom-initialize 'force)
@@ -114,6 +116,8 @@ If passed the prefix ARG, clear the envvar file. Uses the same mechanism as
 An envvar file contains a snapshot of your shell environment, which can be
 imported into Emacs."
   (interactive "P")
+  (when IS-WINDOWS
+    (user-error "Cannot reload envvar file from within Emacs on Windows, run it from cmd.exe"))
   (doom--compile
     (format "%s -c '%s env%s'" shell-file-name doom-bin (if arg " -c" ""))
     :on-success
diff --git a/core/core-cli.el b/core/core-cli.el
index 596449918..6e1aac662 100644
--- a/core/core-cli.el
+++ b/core/core-cli.el
@@ -222,8 +222,9 @@ BODY will be run when this dispatcher is called."
 (defcligroup! "Maintenance"
   "For managing your config and packages"
   (defcli! (refresh re sync)
-    ((if-necessary-p ["-n" "--if-necessary"] "Only regenerate autoloads files if necessary")
-     (prune-p ["-p" "--prune"] "Purge orphaned packages & regraft repos"))
+    ((if-necessary-p   ["-n" "--if-necessary"] "Only regenerate autoloads files if necessary")
+     (inhibit-envvar-p ["-e"] "Don't regenerate the envvar file")
+     (prune-p          ["-p" "--prune"] "Purge orphaned packages & regraft repos"))
     "Ensure Doom is properly set up.
 
 This is the equivalent of running autoremove, install, autoloads, then
@@ -241,7 +242,8 @@ stale."
     (print! (start "Initiating a refresh of Doom Emacs..."))
     (print-group!
      (let (success)
-       (when (file-exists-p doom-env-file)
+       (when (and (not inhibit-envvar-p)
+                  (file-exists-p doom-env-file))
          (doom-cli-reload-env-file 'force))
 
        ;; Ensures that no pre-existing state pollutes the generation of the new