Fixing a Hacked Website the Right Way (Not Just Deleting Files)

Discovering that your website is hacked is stressful. Pages may redirect to spam, browsers might show warning messages, and your reputation can suffer overnight. In the rush to get back online, many teams focus only on deleting visible malware files. Unfortunately, that approach almost always leaves doors open for attackers.

At Upsite Pro we handle website security hardening and malware removal for business-critical sites. In this guide we’ll walk you through a structured way to fix a hacked website so that you minimize downtime and prevent repeat incidents.

Step 1: Contain the incident

Before changing anything, your goal is to prevent further damage:

• Temporarily put the site in maintenance mode if possible.
• Inform your hosting provider so they can help with logs and isolation.
• Change admin passwords and hosting control panel credentials from a secure device.

If your site handles payments or sensitive data, you may also need to consult legal or compliance teams. Quick, transparent communication is better than silence.

Step 2: Take backups and capture evidence

It sounds counterintuitive, but you should create a full backup of your compromised website before you clean anything. This backup is useful to:

• Analyze how attackers got in.
• Compare infected files with clean versions later.
• Provide evidence if you need to work with security specialists.

We often store these backups offline, then work on a separate copy when performing the actual malware removal.

Step 3: Identify the entry point

Cleaning a hacked website without understanding the root cause is like mopping water while a pipe is still leaking. Common attack vectors include:

• Outdated CMS core, themes, or plugins.
• Weak passwords and reused credentials.
• Insecure file permissions or exposed admin panels.
• Vulnerable custom code with SQL injection or file upload flaws.

By reviewing access logs, error logs, and suspicious code patterns, we can narrow down how attackers got in and what they changed.

Step 4: Clean and restore safely

There are several strategies for cleaning a hacked site:

• Restore from a known clean backup and then patch the vulnerability.
• Perform a file-by-file cleanup comparing against original sources where possible.
• Rebuild critical components if the code is too compromised or outdated.

During cleanup we remove malicious scripts, backdoors, injected iframes, and database payloads. We also run targeted scans to detect hidden malware that may not show up in simple antivirus checks.

Step 5: Harden your website and hosting

Once your site is clean and back online, you still need to close the holes that made the attack possible. Our website security services typically include:

• Updating all software, themes, and plugins to secure versions.
• Removing unused or unmaintained extensions.
• Restricting admin access, enforcing strong passwords, and enabling multi-factor authentication where possible.
• Configuring firewalls, rate limiting, and bot protection at the application or hosting level.

We also review database access, file permissions, and backups as part of a broader security hardening effort.

Step 6: Monitor and prepare for the future

Security is not a one-time task. After a major incident, you should have monitoring and incident-response processes in place. This can include:

• Uptime monitoring and alerting.
• Log retention so you can investigate suspicious activity.
• Regular security reviews as part of your website maintenance plan.

By treating security as an ongoing responsibility, you dramatically reduce the chances of a repeat attack and shorten recovery time if something does happen.

Need urgent help with a hacked website?

If your website is hacked right now, you need calm, structured action — not panic. Upsite Pro can help you contain the incident, clean the malware, restore your site, and harden your environment so you can get back to business.