How to Fix a Hacked Website: Step-by-Step Recovery & Protection

Did you know that over 30,000 websites are hacked every day? From small business sites to major brands, no one is immune. A hacked website does not just damage your reputation, it can leak sensitive data, spread malware, and tank your SEO rankings overnight.

But don’t panic. With a systematic approach, you can regain control, clean up the infection, and secure your website to prevent future attacks. This detailed guide walks you through each step of recovering from a website hack, from detection to long-term protection.

Why Quick Action Matters

Every moment your website remains compromised increases the risk of malware spreading, customer data theft, or further exploitation. Prompt detection and cleanup reduce downtime and limit damage.

Is My Site Hacked? How to Know for Sure

Determining whether your site is hacked is often not as straightforward as a defaced homepage or a shutdown. Modern attacks are stealthily designed to persist undetected while extracting value. Watch for these subtle and obvious signs of compromise:

1. Redirects to Unknown or Malicious Websites

If your visitors are being redirected to adult sites, fake giveaways, or phishing pages, this usually means:

• A malicious script (JavaScript, iframe) has been injected into your HTML/PHP.
• .htaccess rules or DNS entries have been modified.
• A redirect is cloaked to avoid detection unless the user is from a search engine (user-agent cloaking).

This is one of the most common signs your site has been hacked, especially for WordPress and eCommerce sites.

2. New Admin Users or Locked-Out Access

Hackers commonly create hidden admin users to retain access even after cleanup. You might notice:

• Unknown usernames with administrator or super admin roles
• Your admin account gets locked, or its password is reset
• Backend access logs show unauthorized login attempts, especially from foreign IPs

Critical Risk: If an attacker has admin privileges, they can edit themes, plugins, or create cron jobs to reinfect your site post-cleanup.

3. Defaced Website or Altered Appearance

The most obvious sign is a homepage that is replaced with a “hacked by” message. But subtler symptoms include:

• Changes in homepage text, banners, or embedded YouTube/Vimeo videos
• Random popups or advertisements not placed by you
• Embedded crypto mining scripts using visitors’ CPUs (cryptojacking)

These are clear red flags if you are trying to recover a hacked WordPress site or CMS-powered application.

4. Sudden Spikes in Traffic or Server Load

Compromised sites are often used in:

• Botnet operations (DDoS attacks)
• SEO spam campaigns (hundreds of spam pages generated in the background)
• Phishing kit hosting

Symptoms may include:

• High CPU usage on your hosting dashboard
• Excessive POST requests or large payloads in logs
• Unexpected bandwidth spikes on cPanel or CDN

Do not ignore these; they often indicate active exploitation.

If you are unsure whether this is a DDoS or botnetinfection, run a malware scan to confirm if your website has been hacked.

5. Google Blacklist Alerts or Browser Warnings

Google and other authorities (like Norton or McAfee) scan for malware and phishing activity. You may see:

• Red “Deceptive Site Ahead” or “Website contains malware” warnings
• Google Search Console messages alerting of a breach
• Organic traffic drops due to removal from search results

Impact: Your SEO rankings may plummet until a security review and reconsideration request is approved.

Immediate Response: Contain the Breach

1. Take the website offline or switch to maintenance mode.
2. Notify your hosting provider — they may help isolate the attack.
3. Create a full backup, including infected files, for forensic review.
4. Start logging events: failed logins, file modifications, and server logs.
5. Reach Out for 24/7 Under-Attack Support – Get expert help to contain the breach quickly and assess the full scope of the attack.

Need Help? Here Is What to Do If Your Website Is Hacked

If you are unsure what to do next, follow this step-by-step guide to clean a hacked website, recover control, and prevent reinfection.

Step 1: Scan for Malware & Zero-Day Exploits

A compromised website may not always exhibit visible signs. Sophisticated attackers hide malware in nested directories, cron jobs, database injections, or third-party scripts. Here is how to approach scanning:

• Use an Automatic website scanner: Tools like Indusface WAS can help detect malicious scripts, suspicious changes, and known exploits. Using an intelligent scanning system, Indusface WAS detects parameterized deviations across multiple parts of your web pages including the DOM, internal links, JavaScript scripts, multimedia elements, and more to pinpoint malware infections or unauthorized defacements that traditional scanners often miss.
• Check Core Files & Directories: Compare current versions of your website’s core CMS files (e.g., WordPress, Joomla) against clean backups or original distributions to spot unauthorized modifications.
• Review Server Logs: Look for unusual requests, spikes in traffic to suspicious pages, or unauthorized admin logins.
• Inspect Database Content: Attackers often inject malicious payloads or backdoors into database tables like wp_options or wp_posts. Use SQL tools or admin dashboards to search for suspicious code snippets.
• Scan for Zero-Day Indicators: Zero-days may exploit unknown vulnerabilities. While harder to detect, keep an eye on abnormal behaviors like file permission changes or newly created admin accounts. Indusface has developed an AI-powered platform that continuously monitors the evolving threat landscape by analyzing diverse threat intelligence feeds. This system filters and prioritizes vulnerabilities relevant to web applications, assesses the availability of proof-of-concept (PoC) exploits, and evaluates their virality and potential impact. This proactive approach enables Indusface WAS to highlight critical zero-day vulnerabilities requiring immediate action, significantly boosting both threat coverage and operational efficiency.

Step 2: Clean the Hacked Website

Once you have identified malware, backdoors, or unauthorized changes, it is time to clean your site and restore it to a secure state:

• Back Up Your Website First: Before making any changes, create a full backup of your website files and database. This ensures you have a recovery point if something goes wrong during cleanup.
• Remove Malicious Files and Code: Manually or with the help of security tools, delete injected malicious scripts, suspicious plugins, unauthorized admin accounts, or any rogue files. Be thorough check core CMS files, themes, plugins, uploads, and custom scripts. Be thorough check core CMS files, themes, plugins, uploads, and custom scripts.
• Restore Clean Versions: Where possible, replace infected files with fresh copies from official sources (e.g., WordPress.org or your CMS vendor). For databases, remove malicious entries or restore from a clean backup.
• Patch Security Vulnerabilities: Identify and fix the vulnerabilities that allowed the attack in the first place by updating outdated CMS, plugins, themes, and server software.
• Instant Virtual Patching: If patching immediately is not possible, use AppTrana SwyftComply to apply instant virtual patches for detected vulnerabilities. This provides immediate protection by blocking exploitation attempts at the application layer until you can complete permanent fixes.
• Check .htaccess and Configuration Files: Attackers often modify server configuration files like .htaccess, web.config, or wp-config.php to maintain control. Compare them with defaults and revert unauthorized changes.
• Reset Passwords: Change passwords for your website admin accounts, hosting control panel, database, and FTP/SFTP accounts. Use strong, unique passwords.
• Scan Again: After cleaning, run a complete malware scan to confirm your website is clean before bringing it back online.

Step 3: Restore from a Clean Backup

If your scans reveal widespread infection or if cleaning individual files is not feasible, restoring your website from a clean backup can be the fastest and safest option. Choose a backup created before the compromise date ideally stored offline or in a secure cloud environment.

• Verify Backup Integrity: Ensure the backup itself is not infected by scanning it before restoration.
• Restore Files & Database: Replace your current website files and database with the clean versions from your backup.
• Test Before Going Live: After restoring, check your website in a staging environment or with maintenance mode enabled to confirm functionality and security.
• Update After Restore: Once restored, immediately apply all pending updates to your CMS, themes, plugins, and server software to close any security gaps that existed at the time of the backup.

Step 4: Secure Your Website from Hackers

Cleaning and restoring your site are not enough, you need to harden it against future attacks:

• Apply Updates Promptly: Keep your CMS, plugins, server, and third-party components updated at all times. Enable automatic updates where possible.
• Strengthen Authentication: Use strong, unique passwords and enable multi-factor authentication (MFA) for all admin accounts.
• Limit Access & Permissions: Remove unused user accounts, restrict admin access by IP, and set proper file permissions to reduce your attack surface.
• Install a Web Application and API Protection: Deploy a solution like AppTrana WAAP to block malicious traffic, stop exploits (including zero-days), and provide instant virtual patching for newly discovered vulnerabilities.
• Schedule Regular Scans: Use Indusface WAS for continuous vulnerability scanning, malware detection, and defacement monitoring with expert-managed support to verify and remediate findings.
• Monitor Logs & Activity: Keep an eye on server, application, and security logs for suspicious activity, such as repeated login failures or unexpected file changes.
• Back Up Regularly: Set up automated, offsite backups of your website files and database, and test them periodically to ensure they’re working as intended.
• Implement Security Headers & CSP: Add HTTP security headers like Content Security Policy (CSP) and X-Frame-Options to protect against common attacks like XSS and clickjacking. Attackers increasingly target third-party scripts to steal payment or personal data directly from customer browsers. AppTrana WAAP helps you mitigate these threats by enforcing security headers like Content Security Policy (CSP) and monitoring for unauthorized changes in JavaScript files, ensuring forms and checkout flows remain secure against client-side exploits.

By following these measures, you not only recover from the hack but also significantly reduce the risk of your website being compromised again.

Step 5: Implement a Response & Recovery Plan

Recovering from a hack is not just about cleaning up; it is about building a repeatable, documented process so your team is ready to respond faster and more effectively next time. Here’s how to do it right:

Document the Incident: Record when and how the hack was discovered, what parts of the website were affected, and what vulnerabilities were exploited. Include details of malware infections, defacements, or unauthorized changes.

Record the Response Actions: Note each step taken during detection, isolation, cleanup, restoration, and security hardening. Include tools used, team members involved, and timeframes for every action.

Establish an Incident Response Playbook: Create a clear, step-by-step guide that outlines how to:

• Identify and confirm an attack.
• Communicate with stakeholders and customers if needed.
• Contain and remediate the threat.
• Restore from backups or clean infected systems.
• Perform root cause analysis to prevent recurrence.

Assign Roles & Responsibilities: Define who does what during a security incident, from technical remediation to legal or PR communications, so there’s no confusion in a crisis.

Review & Update Regularly: After recovery, conduct a post-mortem with your team to identify gaps or bottlenecks in your response and update the playbook accordingly.

A well-defined response and recovery plan reduces downtime, limits damage, and gives your team confidence to act decisively during future incidents.

Step 6: Improve Compliance Readiness

Beyond technical security, a hack can expose gaps in compliance with industry or regulatory standards leaving you open to fines or legal action. Strengthening your compliance posture after an incident is crucial.

Assess Regulatory Requirements: Determine which standards apply to your website and business, such as PCI DSS for payment data, GDPR for EU customers, HIPAA for healthcare information, or industry-specific guidelines.

Conduct a Compliance Gap Analysis: Review your website and supporting infrastructure against these requirements. Identify areas where your security or data protection measures fall short.

Implement Remediation Measures: Address compliance gaps uncovered during your analysis. For example, updating your privacy policy, enabling encryption for sensitive data, or configuring access controls.

Leverage Zero Vulnerability Reports for Proof of Compliance:
Many standards (PCI DSS, SOC 2, ISO 27001, etc.) require proof that you regularly scan for vulnerabilities and maintain a secure environment. Providing a zero-vulnerability report, showing no open vulnerabilities at the time of assessment demonstrates that your website is secure and that you take vulnerability management seriously. These clean reports offer strong evidence of your commitment to security for auditors, partners, and regulators.

Is Your Website Really Safe?
Hackers do not wait. Do not leave your site exposed. Run a free, instant security scan and see what threats you might be missing!

Scan Your Website Now

Stay tuned for more relevant and interesting security articles. Follow Indusface on Facebook, Twitter, and LinkedIn.