WordPress 6.1 has introduced some server-side filters to hook into the theme.json data provided at the different data layers:

• wp_theme_json_data_default: hooks into the default data provided by WordPress
• wp_theme_json_data_blocks: hooks into the data provided by the blocks
• wp_theme_json_data_theme: hooks into the data provided by the theme
• wp_theme_json_data_user: hooks into the data provided by the user

Each filter receives an instance of the WP_Theme_JSON_Data class with the data for the respective layer. To provide new data, the filter callback needs to use the update_with( $new_data ) method, where $new_data is a valid theme.json-like structure. As with any theme.json, the new data needs to declare which version of the theme.json is using, so it can correctly be migrated to the runtime one, should it be different.

Example:

This is how to pass a new color palette for the theme and disable the text color UI:

function wpdocs_filter_theme_json_theme( $theme_json ){
    $new_data = array(
        'version'  => 2,
        'settings' => array(
            'color' => array(
                'text'       => false,
                'palette'    => array( /* New palette */
                    array(
                        'slug'  => 'foreground',
                        'color' => 'black',
                        'name'  => __( 'Foreground', 'theme-domain' ),
                    ),
                    array(
                        'slug'  => 'background',
                        'color' => 'white',
                        'name'  => __( 'Background', 'theme-domain' ),
                    ),
                ),
            ),
        ),
    );

    return $theme_json->update_with( $new_data );
}
add_filter( 'wp_theme_json_data_theme', 'wpdocs_filter_theme_json_theme' );