diff --git a/projects/plugins/jetpack/modules/custom-css/custom-css/js/core-customizer-css.core-4.9.js b/projects/plugins/jetpack/modules/custom-css/custom-css/js/core-customizer-css.core-4.9.js
index 1e81f9e0ebba3..ee1b37e9273cf 100644
--- a/projects/plugins/jetpack/modules/custom-css/custom-css/js/core-customizer-css.core-4.9.js
+++ b/projects/plugins/jetpack/modules/custom-css/custom-css/js/core-customizer-css.core-4.9.js
@@ -58,7 +58,7 @@
 		}
 
 		// Show deprecation warning if Start Fresh option is enabled
-		if ( !! window._jp_css_settings.startFresh ) {
+		if ( !! window._jp_css_settings.startFresh && window._currentSiteType !== 'atomic' ) {
 			customize.notifications.add( new customize.Notification( 'start-fresh-warning', {
 				message: window._jp_css_settings.l10n.startFreshCustomizerWarning,
 				type: 'warning',