Discovering that your WordPress site has been hacked can be alarming, but having access to cPanel, WP Toolkit, Imunify360, and JetBackup gives you a complete set of tools to isolate, clean, and restore your site safely.
Step 1: Isolate the Site & Enable Maintenance Mode
Before starting any cleanup, isolate the site to prevent malware from infecting visitors or spreading across other domains in your account.
- Log in to your cPanel dashboard.
- Under the Domains or Applications section, click on WP Toolkit.

- Locate your affected WordPress installation.
- Toggle Maintenance Mode to ON. This stops public visitors from hitting malicious redirects while you work.
- In WP Toolkit, click Check WordPress Integrity. This compares your core files against official WordPress.org hashes to flag modified core files.
Step 2: Scan and Clean Malware with Imunify360
Imunify360 is built directly into cPanel to locate and neutralise malicious PHP scripts, webshells, and injected code.
- Return to the main cPanel Tools page and scroll down to the Security section.
- Click on Imunify360.

- Open the Malware Scanner tab.
- Click Start scanning to perform a deep scan of your home directory.
- Once the scan completes:
- Review the list of infected files under Malicious.
- Click Clean up all (or the individual gear icon next to each infected file) to automatically remove injected payload code or quarantine malicious standalone scripts.
Step 3: Restore from a Clean Backup (If Needed)
If the site remains broken after cleaning, or if malware modified too many core/theme files, roll back to a clean state using JetBackup.
- In cPanel, navigate to the Files section and select JetBackup.

- Choose File Backups or WordPress Backups:
- Select a restore point from 2–5 days ago (before the hack occurred).
- Click Restore next to your chosen date.
3. Next, select Database Backups in JetBackup and restore the database corresponding to that same clean date.
Note: Restoring a backup will revert any posts or page changes made after that backup date, but it guarantees a known clean file system.
Step 4: Audit Users & Change Credentials
Once the site is back up and clean, secure all access points so the attacker cannot return:
1. Audit WordPress Users
- Open WP Toolkit or log into /wp-admin/.
- Go to Users and remove any administrator accounts you don't recognise. Attackers often create stealth admin users (e.g., system_admin, wp_support).
2. Reset All Passwords
- Change your cPanel account password.
- Change your WordPress Admin passwords (you can force a password reset directly from WP Toolkit under the Setup menu without logging into wp-admin).
- Change your Database user password via cPanel's MySQL Databases page (remember to update the DB_PASSWORD inside wp-config.php if you change this).
3. Reinstall Fresh Plugins and Themes
- Go to WP Toolkit -> Plugins / Themes.
- Update all plugins and themes to their latest versions to patch known security vulnerabilities.
- Remove any inactive plugins or nulled/pirated themes, as these are the primary vector for backdoors.
Step 5: Hardening & Prevention
To ensure the hack doesn't reoccur:
- Enable Automatic Updates: In WP Toolkit, enable Autoupdate settings for WordPress Core, Plugins, and Themes.
- Run Security Measures: In WP Toolkit, click Security and apply recommended measures (such as restricting access to xmlrpc.php, blocking directory browsing, and forcing HTTPS).
- Reset Security Keys (Salts): Generate new secret keys in your wp-config.php file (or use WP Toolkit's security hardening options) to invalidate all active session cookies across the web.