diff --git a/core/core-fonts-support.el b/core/core-fonts-support.el
index 8da498fe55c8..ebe00726d70e 100644
--- a/core/core-fonts-support.el
+++ b/core/core-fonts-support.el
@@ -49,7 +49,16 @@ The return value is nil if no font was found, truthy otherwise."
                             :powerline-offset))
                (fontspec (apply 'font-spec :name font font-props)))
           (spacemacs-buffer/message "Setting font \"%s\"..." font)
-          (set-frame-font fontspec nil t)
+          ;; We set the INHIBIT-CUSTOMIZE parameter to t to tell set-frame-font
+          ;; not to fiddle with the default face in the user's Customization
+          ;; settings. We don't need Customization because our way of ensuring
+          ;; that the font is applied to future frames is to modify
+          ;; default-frame-alist, and Customization causes issues, see
+          ;; https://github.com/syl20bnr/spacemacs/issues/5353.
+          ;; INHIBIT-CUSTOMIZE is only present in recent emacs versions. 
+          (if (version< emacs-version "28.0.90")
+              (set-frame-font fontspec nil t)
+            (set-frame-font fontspec nil t t))
           (push `(font . ,(frame-parameter nil 'font)) default-frame-alist)
           ;; fallback font for unicode characters used in spacemacs
           (pcase system-type