diff --git a/wp-includes/class-wp-theme-json.php b/wp-includes/class-wp-theme-json.php
index 1d92e5c35a..a893dfb6a9 100644
--- a/wp-includes/class-wp-theme-json.php
+++ b/wp-includes/class-wp-theme-json.php
@@ -429,6 +429,38 @@ class WP_Theme_JSON {
 		),
 	);
 
+	/*
+	 * The valid properties for fontFamilies under settings key.
+	 *
+	 * @since 6.5.0
+	 *
+	 * @var array
+	 */
+	const FONT_FAMILY_SCHEMA = array(
+		array(
+			'fontFamily' => null,
+			'name'       => null,
+			'slug'       => null,
+			'fontFace'   => array(
+				array(
+					'ascentOverride'        => null,
+					'descentOverride'       => null,
+					'fontDisplay'           => null,
+					'fontFamily'            => null,
+					'fontFeatureSettings'   => null,
+					'fontStyle'             => null,
+					'fontStretch'           => null,
+					'fontVariationSettings' => null,
+					'fontWeight'            => null,
+					'lineGapOverride'       => null,
+					'sizeAdjust'            => null,
+					'src'                   => null,
+					'unicodeRange'          => null,
+				),
+			),
+		),
+	);
+
 	/**
 	 * The valid properties under the styles key.
 	 *
@@ -556,6 +588,52 @@ class WP_Theme_JSON {
 		'typography'           => 'typography',
 	);
 
+	/**
+	 * Return the input schema at the root and per origin.
+	 *
+	 * @since 6.5.0
+	 *
+	 * @param array $schema The base schema.
+	 * @return array The schema at the root and per origin.
+	 *
+	 * Example:
+	 * schema_in_root_and_per_origin(
+	 *   array(
+	 *    'fontFamily' => null,
+	 *    'slug' => null,
+	 *   )
+	 * )
+	 *
+	 * Returns:
+	 * array(
+	 *  'fontFamily' => null,
+	 *  'slug' => null,
+	 *  'default' => array(
+	 *    'fontFamily' => null,
+	 *    'slug' => null,
+	 *  ),
+	 *  'blocks' => array(
+	 *    'fontFamily' => null,
+	 *    'slug' => null,
+	 *  ),
+	 *  'theme' => array(
+	 *     'fontFamily' => null,
+	 *     'slug' => null,
+	 *  ),
+	 *  'custom' => array(
+	 *     'fontFamily' => null,
+	 *     'slug' => null,
+	 *  ),
+	 * )
+	 */
+	protected static function schema_in_root_and_per_origin( $schema ) {
+		$schema_in_root_and_per_origin = $schema;
+		foreach ( static::VALID_ORIGINS as $origin ) {
+			$schema_in_root_and_per_origin[ $origin ] = $schema;
+		}
+		return $schema_in_root_and_per_origin;
+	}
+
 	/**
 	 * Returns a class name by an element name.
 	 *
@@ -797,11 +875,12 @@ class WP_Theme_JSON {
 			$schema_styles_blocks[ $block ]['variations'] = $schema_styles_variations;
 		}
 
-		$schema['styles']             = static::VALID_STYLES;
-		$schema['styles']['blocks']   = $schema_styles_blocks;
-		$schema['styles']['elements'] = $schema_styles_elements;
-		$schema['settings']           = static::VALID_SETTINGS;
-		$schema['settings']['blocks'] = $schema_settings_blocks;
+		$schema['styles']                                 = static::VALID_STYLES;
+		$schema['styles']['blocks']                       = $schema_styles_blocks;
+		$schema['styles']['elements']                     = $schema_styles_elements;
+		$schema['settings']                               = static::VALID_SETTINGS;
+		$schema['settings']['blocks']                     = $schema_settings_blocks;
+		$schema['settings']['typography']['fontFamilies'] = static::schema_in_root_and_per_origin( static::FONT_FAMILY_SCHEMA );
 
 		// Remove anything that's not present in the schema.
 		foreach ( array( 'styles', 'settings' ) as $subtree ) {
@@ -974,18 +1053,39 @@ class WP_Theme_JSON {
 	 * @return array The modified $tree.
 	 */
 	protected static function remove_keys_not_in_schema( $tree, $schema ) {
-		$tree = array_intersect_key( $tree, $schema );
+		if ( ! is_array( $tree ) ) {
+			return $tree;
+		}
 
-		foreach ( $schema as $key => $data ) {
-			if ( ! isset( $tree[ $key ] ) ) {
+		foreach ( $tree as $key => $value ) {
+			// Remove keys not in the schema or with null/empty values.
+			if ( ! array_key_exists( $key, $schema ) ) {
+				unset( $tree[ $key ] );
 				continue;
 			}
 
-			if ( is_array( $schema[ $key ] ) && is_array( $tree[ $key ] ) ) {
-				$tree[ $key ] = static::remove_keys_not_in_schema( $tree[ $key ], $schema[ $key ] );
+			// Check if the value is an array and requires further processing.
+			if ( is_array( $value ) && is_array( $schema[ $key ] ) ) {
+				// Determine if it is an associative or indexed array.
+				$schema_is_assoc = self::is_assoc( $value );
 
-				if ( empty( $tree[ $key ] ) ) {
-					unset( $tree[ $key ] );
+				if ( $schema_is_assoc ) {
+					// If associative, process as a single object.
+					$tree[ $key ] = self::remove_keys_not_in_schema( $value, $schema[ $key ] );
+
+					if ( empty( $tree[ $key ] ) ) {
+						unset( $tree[ $key ] );
+					}
+				} else {
+					// If indexed, process each item in the array.
+					foreach ( $value as $item_key => $item_value ) {
+						if ( isset( $schema[ $key ][0] ) && is_array( $schema[ $key ][0] ) ) {
+							$tree[ $key ][ $item_key ] = self::remove_keys_not_in_schema( $item_value, $schema[ $key ][0] );
+						} else {
+							// If the schema does not define a further structure, keep the value as is.
+							$tree[ $key ][ $item_key ] = $item_value;
+						}
+					}
 				}
 			} elseif ( is_array( $schema[ $key ] ) && ! is_array( $tree[ $key ] ) ) {
 				unset( $tree[ $key ] );
@@ -995,6 +1095,20 @@ class WP_Theme_JSON {
 		return $tree;
 	}
 
+	/**
+	 * Checks if the given array is associative.
+	 *
+	 * @since 6.5.0
+	 * @param array $data The array to check.
+	 * @return bool True if the array is associative, false otherwise.
+	 */
+	protected static function is_assoc( $data ) {
+		if ( array() === $data ) {
+			return false;
+		}
+		return array_keys( $data ) !== range( 0, count( $data ) - 1 );
+	}
+
 	/**
 	 * Returns the existing settings for each block.
 	 *
diff --git a/wp-includes/version.php b/wp-includes/version.php
index 3e9ac5f09f..ad47881563 100644
--- a/wp-includes/version.php
+++ b/wp-includes/version.php
@@ -16,7 +16,7 @@
  *
  * @global string $wp_version
  */
-$wp_version = '6.5-alpha-57495';
+$wp_version = '6.5-alpha-57496';
 
 /**
  * Holds the WordPress DB revision, increments when changes are made to the WordPress DB schema.