diff --git a/core/core-packages.el b/core/core-packages.el
index bfcbcaae8..02389a85b 100644
--- a/core/core-packages.el
+++ b/core/core-packages.el
@@ -308,7 +308,7 @@ MODULES is an malformed plist of modules to load."
   (let (init-forms config-forms module file-name-handler-alist)
     (let ((modules-dir
            (expand-file-name "modules/" (file-name-directory (or load-file-name byte-compile-current-file)))))
-      (add-to-list 'doom-modules-dirs modules-dir)
+      (cl-pushnew modules-dir doom-modules-dirs :test #'string=)
       (dolist (m modules)
         (cond ((keywordp m) (setq module m))
               ((not module) (error "No namespace specified in `doom!' for %s" m))
@@ -323,8 +323,8 @@ MODULES is an malformed plist of modules to load."
          (setq doom-modules ',doom-modules
                doom-modules-dirs ',doom-modules-dirs)
          ,@(nreverse init-forms)
-         (unless noninteractive
-           ,@(nreverse config-forms))))))
+         (push '(lambda () ,@(nreverse config-forms))
+               doom--delayed-modules)))))
 
 (defmacro def-package! (name &rest plist)
   "A thin wrapper around `use-package'."
diff --git a/core/core.el b/core/core.el
index eab311343..bb56cddd9 100644
--- a/core/core.el
+++ b/core/core.el
@@ -119,6 +119,8 @@ Use this for essential functionality.")
   "A list of hooks run after DOOM initialization is complete, and after
 `doom-init-hook'. Use this for extra, non-essential functionality.")
 
+(defvar doom--delayed-modules nil)
+
 (defun doom-try-run-hook (fn hook)
   "Runs a hook wrapped in a `condition-case-unless-debug' block; its objective
 is to include more information in the error message, without sacrificing your
@@ -139,8 +141,8 @@ ability to invoke the debugger in debug mode."
 (eval-and-compile
   (defvar doom--file-name-handler-alist file-name-handler-alist)
   (unless (or after-init-time noninteractive)
-    ;; One of the contributors to long startup times is the garbage collector,
-    ;; so we up its memory threshold, temporarily. It is reset later in
+    ;; A big contributor to long startup times is the garbage collector, so we
+    ;; up its memory threshold, temporarily and reset it later in
     ;; `doom|finalize'.
     (setq gc-cons-threshold 402653184
           gc-cons-percentage 0.6
@@ -156,9 +158,15 @@ ability to invoke the debugger in debug mode."
     (load! core-projects)   ; making Emacs project-aware
     (load! core-keybinds))  ; centralized keybind system + which-key
 
-  (defun doom|finalize ()
-    "Run `doom-init-hook', `doom-post-init-hook' and reset `gc-cons-threshold',
-`gc-cons-percentage' and `file-name-handler-alist'."
+  (defun doom|after-init ()
+    "Load the config.el file of all pending modules that have been enabled by a
+recent `doom!' call. This should be attached to `after-init-hook'."
+    (mapc #'funcall (reverse doom--delayed-modules))
+    (setq doom--delayed-modules nil))
+
+  (defun doom|after-startup ()
+    "Run `doom-init-hook' and `doom-post-init-hook', start the Emacs server, and
+display the loading benchmark."
     (unless (or (not after-init-time) noninteractive)
       (dolist (hook '(doom-init-hook doom-post-init-hook))
         (run-hook-wrapped hook #'doom-try-run-hook hook))
@@ -166,15 +174,20 @@ ability to invoke the debugger in debug mode."
         (require 'server)
         (unless (server-running-p)
           (server-start)))
-      (message "%s" (doom-packages--benchmark)))
-    ;; If you forget to reset this, you'll get stuttering and random freezes!
+      (message "%s" (doom-packages--benchmark))))
+
+  (defun doom|finalize ()
+    "Resets garbage collection settings to reasonable defaults (if you don't do
+this, you'll get stuttering and random freezes), and resets
+`file-name-handler-alist'."
     (setq gc-cons-threshold 16777216
           gc-cons-percentage 0.1
           file-name-handler-alist doom--file-name-handler-alist)
     t)
 
-  (add-hook! '(emacs-startup-hook doom-reload-hook)
-    #'doom|finalize))
+  (add-hook! '(emacs-startup-hook doom-reload-hook) #'doom|finalize)
+  (add-hook 'after-init-hook    #'doom|after-init)
+  (add-hook 'emacs-startup-hook #'doom|after-startup))
 
 
 ;;