WordPress shows I have 1 plugin update, when all plugins are already updated

I see this from time to time with premium plugins and themes that require an activation key. The WP UI won’t provide anyway to update the plugin or theme, but you’ll see the pending update count number in the UI.

To track down the source I use the following function:

/**
 * Debug Pending Updates
 *
 * Crude debugging method that will spit out all pending plugin
 * and theme updates for admin level users when ?debug_updates is
 * added to a /wp-admin/ URL.
 */
function debug_pending_updates() {

    // Rough safety nets
    if ( ! is_user_logged_in() || ! current_user_can( 'manage_options' ) ) return;
    if ( ! isset( $_GET['debug_updates'] ) ) return;

    $output = "";

    // Check plugins
    $plugin_updates = get_site_transient( 'update_plugins' );
    if ( $plugin_updates && ! empty( $plugin_updates->response ) ) {
        foreach ( $plugin_updates->response as $plugin => $details ) {
            $output .= "<p><strong>Plugin</strong> <u>$plugin</u> is reporting an available update.</p>";
        }
    }

    // Check themes
    wp_update_themes();
    $theme_updates = get_site_transient( 'update_themes' );
    if ( $theme_updates && ! empty( $theme_updates->response ) ) {
        foreach ( $theme_updates->response as $theme => $details ) {
            $output .= "<p><strong>Theme</strong> <u>$theme</u> is reporting an available update.</p>";
        }
    }

    if ( empty( $output ) ) $output = "No pending updates found in the database.";

    wp_die( $output );
}
add_action( 'init', 'debug_pending_updates' );

Add that to your theme’s functions.php file then visit a page with ?debug_updates added to the URL. For example: yourdomain.example/wp-admin/?debug_updates. This should show you any theme or plugin that’s causing the issue.