diff --git a/core/autoload/config.el b/core/autoload/config.el
index 2e00de8ff..2c61d176e 100644
--- a/core/autoload/config.el
+++ b/core/autoload/config.el
@@ -33,11 +33,11 @@ Runs `doom-reload-hook' afterwards."
     (when (getenv "DOOMENV")
       (doom-reload-env-file 'force))
     (doom-reload-autoloads force-p)
-    (setq load-path doom-site-load-path)
     (let (doom-init-p)
       (doom-initialize))
     (with-demoted-errors "PRIVATE CONFIG ERROR: %s"
-      (doom-initialize-modules 'force))
+      (let (doom-init-modules-p)
+        (doom-initialize-modules)))
     (when (bound-and-true-p doom-packages)
       (doom/reload-packages))
     (run-hook-wrapped 'doom-reload-hook #'doom-try-run-hook))
diff --git a/core/core-modules.el b/core/core-modules.el
index f2185c66d..75d6ed623 100644
--- a/core/core-modules.el
+++ b/core/core-modules.el
@@ -59,6 +59,7 @@ session of Dooming. Will noop if used more than once, unless FORCE-P is
 non-nil."
   (when (and (or force-p
                  (not doom-init-modules-p))
+             (not (setq doom-modules nil))
              (load! "init" doom-private-dir t))
     (setq doom-init-modules-p t)
     (maphash (lambda (key plist)
diff --git a/core/core.el b/core/core.el
index 0dc7a8f4a..e9a797283 100644
--- a/core/core.el
+++ b/core/core.el
@@ -98,11 +98,21 @@ MacOS users).")
   "If non-nil, the running version of Emacs is different from the first time
 Doom was setup, which can cause problems.")
 
-(defvar doom-site-load-path load-path
-  "The starting `load-path', before it is altered by `doom-initialize'.")
+(defvar doom-site-load-path (cons doom-core-dir load-path)
+  "The initial value of `load-path', before it was altered by
+`doom-initialize'.")
 
 (defvar doom-site-process-environment process-environment
-  "The starting `process-environment', before it is altered by `doom-initialize'.")
+  "The initial value of `process-environment', before it was altered by
+`doom-initialize'.")
+
+(defvar doom-site-exec-path exec-path
+  "The initial value of `exec-path', before it was altered by
+`doom-initialize'.")
+
+(defvar doom-site-shell-file-name shell-file-name
+  "The initial value of `shell-file-name', before it was altered by
+`doom-initialize'.")
 
 (defvar doom--last-emacs-file (concat doom-local-dir "emacs-version.el"))
 (defvar doom--last-emacs-version nil)
@@ -431,6 +441,12 @@ to least)."
   (when (or force-p (not doom-init-p))
     (setq doom-init-p t)  ; Prevent infinite recursion
 
+    ;; Reset as much state as possible
+    (setq exec-path doom-site-exec-path
+          load-path doom-site-load-path
+          process-environment doom-site-process-environment
+          shell-file-name doom-site-shell-file-name)
+
     ;; `doom-autoload-file' tells Emacs where to load all its autoloaded
     ;; functions from. This includes everything in core/autoload/*.el and all
     ;; the autoload files in your enabled modules.