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How to Detect and Remove Malware From Your Website Print

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How to Detect and Remove Malware From Your Website

Malware infections can affect any website — even small ones with little traffic. This guide teaches you how to detect, clean, and protect your site from malware, step by step, even if you are not technical.

Tags: malware removal, hacked site, virus scan, wordpress cleanup, beginner security, nairahost

❗ What Is Website Malware?

“Malware” means malicious software. On websites, this usually means code that was added by a hacker without your permission. Malware can hide in your files, themes, plugins, database, or even inside your hosting account.

Common Malware Types

  • Hidden injected code
  • Redirect scripts
  • Phishing pages
  • Backdoor shells
  • Spam content and ads
  • Keyloggers
  • Crypto miners
⚠️ Most malware is invisible on the surface. Your site may appear normal to you while spreading spam or collecting stolen data.

❗ How to Know If Your Website Is Infected

Your site may be hacked if any of these happen:

  • Website redirects somewhere else
  • Unknown links, ads or pop-up appears
  • Admin account added without your permission
  • Google shows “This site may be harmful” warning
  • Your email is sending spam
  • Hosting CPU usage is unusually high
  • Files appear that you did not create
  • Your hosting company automatically suspended you
⚠️ A malware infection will NOT fix itself. The longer you ignore it, the worse the damage becomes.

✔️ Step 1: Scan Your Website for Malware

You should run both an external scan AND an internal scan.

External Online Malware Scanners

  • SiteCheck by Sucuri
  • VirusTotal URL Scan
  • Google Safe Browsing Diagnostic

Internal Malware Scanners

For WordPress users:

  • Wordfence malware scanner
  • iThemes Security scanner
  • MalCare plugin
✔️ External scanners cannot see everything. They can only detect visible or public malware. Internal scans are more accurate.

✔️ Step 2: Make a Backup of Your Website

Before cleaning, always make a backup — even if your site is infected. This allows you to restore or manually inspect files later.

Use:

  • cPanel File Manager ZIP backup
  • JetBackup (if available)
  • UpdraftPlus (WordPress)
⚠️ Never delete files randomly without backup — you may break your site further.

✔️ Step 3: Clean the Infection (Beginner-Safe Methods)

Method 1: Automatic Malware Cleaning (WordPress)

Recommended tools:

  • Wordfence → Scan → Repair files
  • MalCare → Auto-clean
  • iThemes Security → File change scan
✔️ Wordfence FREE version can clean most infections automatically if the original WordPress core files were modified.

Method 2: Replace Core Files Manually

If only WordPress core files are infected:

  1. Download a fresh copy of WordPress from wordpress.org
  2. Delete wp-admin and wp-includes on your server
  3. Upload the clean ones in their place
  4. Do NOT replace wp-content or wp-config.php

Method 3: Clean Files by Hand (Advanced but Necessary Sometimes)

Common malicious code patterns include:

eval(base64_decode(...))
gzinflate...
preg_replace('/e'
system($_GET["cmd"])
⚠️ If you do not understand PHP or code, do NOT try to manually edit infected code. Use a security plugin or request support.

✔️ Step 4: Scan and Clean the Database

Malware can also hide inside your database, often inside:

  • wp_posts table
  • wp_options table
  • Injected JavaScript code
  • Hidden backlinks
✔️ If malware keeps coming back after file cleanup, it is almost always stored in your database.

❗ Step 5: Remove Backdoors

Malware often leaves behind “backdoor” scripts so the hacker can get back into your site.

These can hide in:

  • /uploads
  • /wp-includes
  • /wp-content/themes/
  • /wp-content/plugins/
  • randomly named .php files
⚠️ If you do not remove ALL backdoors, the hacker will return even after you clean the site.

⚙️ Step 6: Change All Passwords

After cleaning, change these immediately:

  • WordPress login
  • cPanel / DirectAdmin
  • FTP / File Manager
  • Database user
  • Email accounts
✔️ Use strong, unique passwords and enable 2FA wherever possible.

✔️ Step 7: Re-Scan After Cleaning

Scan again using both:

  • External tool like Sucuri SiteCheck
  • Internal scanner like Wordfence

If everything is clean, the site should now be safe.

❗ If Your Website Was Blacklisted by Google

Once malware is gone:

  1. Sign in to Google Search Console
  2. Verify your domain (if not already done)
  3. Go to Security Issues
  4. Request review after confirming cleanup
⚠️ A hacked website can lose ALL SEO ranking if not cleaned quickly. Time matters.

✔️ How to Prevent Future Malware Infections

  • Use a security plugin and enable auto-blocking
  • Never use nulled themes or plugins
  • Update WordPress regularly
  • Use 2FA on all admin logins
  • Disable file editing
  • Install SSL and force HTTPS

⚙️ What Nairahost Does to Help Protect You

  • Firewall protection at the server level
  • Malware scanning in the background
  • Account isolation — infected sites can’t spread to others
  • Free SSL certificates
  • Secure nameservers:
    cPanel: ns1.nairahost.cloud / ns2.nairahost.cloud
    DirectAdmin: ns1.nairahost.com.ng / ns2.nairahost.com.ng

✔️ Final Malware Removal Checklist

  • ✔️ Website scanned
  • ✔️ Backup created before cleaning
  • ✔️ Infected files removed or replaced
  • ✔️ All passwords changed
  • ✔️ Database checked
  • ✔️ Backdoors removed
  • ✔️ Security plugin installed
  • ✔️ Google review submitted (if blacklisted)
  • ✔️ Regular backups enabled

Malware is scary, but it is not the end of the world. With the steps in this guide, even beginners can detect and remove most website infections, protect their hosting account, and prevent future hacks. The key is simple: scan, clean, reset passwords, and secure your site properly so it never happens again.


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