diff --git a/lib/class-wp-theme-json-gutenberg.php b/lib/class-wp-theme-json-gutenberg.php
index ad4a9f21872be..621e75cfcfb05 100644
--- a/lib/class-wp-theme-json-gutenberg.php
+++ b/lib/class-wp-theme-json-gutenberg.php
@@ -741,7 +741,7 @@ public function __construct( $theme_json = array( 'version' => WP_Theme_JSON_Gut
 			$origin = 'theme';
 		}
 
-		$this->theme_json    = WP_Theme_JSON_Schema_Gutenberg::migrate( $theme_json );
+		$this->theme_json    = WP_Theme_JSON_Schema_Gutenberg::migrate( $theme_json, $origin );
 		$registry            = WP_Block_Type_Registry::get_instance();
 		$valid_block_names   = array_keys( $registry->get_all_registered() );
 		$valid_element_names = array_keys( static::ELEMENTS );
diff --git a/lib/class-wp-theme-json-resolver-gutenberg.php b/lib/class-wp-theme-json-resolver-gutenberg.php
index a02ae74a91fda..18422b290f8ca 100644
--- a/lib/class-wp-theme-json-resolver-gutenberg.php
+++ b/lib/class-wp-theme-json-resolver-gutenberg.php
@@ -534,6 +534,7 @@ public static function get_user_data() {
 				isset( $decoded_data['isGlobalStylesUserThemeJSON'] ) &&
 				$decoded_data['isGlobalStylesUserThemeJSON']
 			) {
+				unset( $decoded_data['isGlobalStylesUserThemeJSON'] );
 				$config = $decoded_data;
 			}
 		}
@@ -542,9 +543,6 @@ public static function get_user_data() {
 		$theme_json = apply_filters( 'wp_theme_json_data_user', new WP_Theme_JSON_Data_Gutenberg( $config, 'custom' ) );
 		$config     = $theme_json->get_data();
 
-		// Needs to be set for schema migrations of user data.
-		$config['isGlobalStylesUserThemeJSON'] = true;
-
 		static::$user = new WP_Theme_JSON_Gutenberg( $config, 'custom' );
 
 		return static::$user;
diff --git a/lib/class-wp-theme-json-schema-gutenberg.php b/lib/class-wp-theme-json-schema-gutenberg.php
index 43b6ea6dcc741..64df6ba7e4b9f 100644
--- a/lib/class-wp-theme-json-schema-gutenberg.php
+++ b/lib/class-wp-theme-json-schema-gutenberg.php
@@ -40,11 +40,13 @@ class WP_Theme_JSON_Schema_Gutenberg {
 	 * @since 5.9.0
 	 * @since 6.6.0 Migrate up to v3.
 	 *
-	 * @param array $theme_json The structure to migrate.
+	 * @param array  $theme_json The structure to migrate.
+	 * @param string $origin     Optional. What source of data this object represents.
+	 *                           One of 'default', 'theme', or 'custom'. Default 'theme'.
 	 *
 	 * @return array The structure in the last version.
 	 */
-	public static function migrate( $theme_json ) {
+	public static function migrate( $theme_json, $origin = 'theme' ) {
 		if ( ! isset( $theme_json['version'] ) ) {
 			$theme_json = array(
 				'version' => WP_Theme_JSON::LATEST_SCHEMA,
@@ -57,7 +59,7 @@ public static function migrate( $theme_json ) {
 				$theme_json = self::migrate_v1_to_v2( $theme_json );
 				// Deliberate fall through. Once migrated to v2, also migrate to v3.
 			case 2:
-				$theme_json = self::migrate_v2_to_v3( $theme_json );
+				$theme_json = self::migrate_v2_to_v3( $theme_json, $origin );
 		}
 
 		return $theme_json;
@@ -104,10 +106,12 @@ private static function migrate_v1_to_v2( $old ) {
 	 * @since 6.6.0
 	 *
 	 * @param array $old Data to migrate.
+	 * @param string $origin     What source of data this object represents.
+	 *                           One of 'default', 'theme', or 'custom'.
 	 *
 	 * @return array Data with defaultFontSizes set to false.
 	 */
-	private static function migrate_v2_to_v3( $old ) {
+	private static function migrate_v2_to_v3( $old, $origin ) {
 		// Copy everything.
 		$new = $old;
 
@@ -118,10 +122,7 @@ private static function migrate_v2_to_v3( $old ) {
 		 * Remaining changes do not need to be applied to the custom origin,
 		 * as they should take on the value of the theme origin.
 		 */
-		if (
-			isset( $new['isGlobalStylesUserThemeJSON'] ) &&
-			true === $new['isGlobalStylesUserThemeJSON']
-		) {
+		if ( 'custom' === $origin ) {
 			return $new;
 		}