How To Detect Malware and Remove It from Your Website

Key takeaways 

• Early malware detection is crucial to protect your customers and your business reputation. 
• Partner with a reputable security service provider to effeciently learn how to detect malware, effectively remove it, and prevent malicious software from ruining your website. 
• Malware prevention is a continuous process, so you should always monitor your website even after malware is removed. 

Launching your own business website is exciting and fulfilling. But suddenly, your site begins to slow down, and all your website data is stolen. What just happened?  Your website is infected with malware. 

AVG suggests that here are 190,000 new malware attacks per second. It’s possibly a broad estimate, but you get the gist: No website is completely immune to malware attacks. Knowing how to detect malware early is key to keeping your online presence safe and your customers’ trust intact. 

In this guide, we’ll show you how to spot malware on your website, safely remove it, and protect your site from future attacks. 

What is malware and why should you care? 

Malware is a broad term for malicious software designed to harm your website or steal information. Common types include viruses, ransomware, spyware, and trojans. Each of these has its own way of causing trouble. 

If your business website is infected with malware, your customers may see strange pop-ups. They may also be redirected to unsafe sites, and sensitive customer data gets compromised. Worse, malware infections can cause your site to be blacklisted by search engines which drives away visitors and hurts your sales. 

Watch out for signs like unexpected slowdowns, odd changes to your site content, sudden spikes in traffic that look suspicious, or warnings from your web host or Google Search Console. Spotting these early helps you act fast before serious damage happens. 

How to detect malware on your website 

There are several ways to detect malware on your business website, including both automated scanning tools and manual checks. Combining these methods provides a more comprehensive approach to identifying and addressing malware threats. 

Here’s how you can get started: 

1. Automated scanning 

These are website security tools you can use to constantly scan for malicious software attacking your website. Since these are automated, you only need to check reports and notifications for malware attacks. These are the tools you can consider: 

• Malware scanners 
  Start by using automated malware scanners such as Malwarebytes, SiteLock, or Sucuri. These tools scan your website’s files and code for known malware signatures and suspicious patterns. They automatically check for malicious software, giving you a heads-up on potential threats before they can escalate. Tools like  SiteLock, a service offered by Network Solutions, provides solid defense against them.  It continuously scans your site for malware, vulnerabilities, and suspicious activity. Once activated, SiteLock starts automatic daily scans without you needing to lift a finger. SiteLock will notify you immediately if it detects malware or other threats. It shows exactly which files or pages are affected. 
• Web Application Firewalls (WAFs) 
  Another automated tool you should consider is a Web Application Firewall (WAF). WAFs actively monitor incoming traffic, filtering out malicious requests before they even reach your website. They help block malicious code and requests from known bad actors, preventing malware from infiltrating your site. 
• Regular scans and server-side detection 
  Schedule regular scans of your website, either daily or weekly, to ensure that new or evolving threats are detected early. A server-side malware scan is especially useful because it can catch infections before they even affect your website’s user interface, ensuring your visitors don’t encounter issues. 

2. Manual checks 

While automated tools are powerful, manual checks allow you to dig deeper and spot more complex or hidden malware infections that might not be detected immediately. 

Here’s how to manually scan your website for malware: 

• Look for unusual website behavior   
  If your site suddenly loads slowly, crashes often, shows strange ads, or redirect visitors to unfamiliar pages? These can be indicators that malware has altered your site. 
• Check website files 
  Access your website files using a file transfer protocol (FTP) client or your web hosting file manager. Look for any suspicious files or alterations. If there are files with unusual names or unfamiliar code, it could signal a malware infection. 
• Examine site code 
  Malicious code often hides in scripts or iframe tags. Carefully inspect your site’s code, especially in scripts or iframe attributes, for any unfamiliar commands or links that could indicate malware injections.  
  • For example, if you notice new files with strange names (like wp-config-old.php or temp123.js) or scripts that include unfamiliar code such as long strings of random characters or unfamiliar links to suspicious websites, that’s a red flag.
  • Also, look for code snippets that start with unusual commands like eval(), base64_decode(), or iframe tags pointing to unknown sources. These red flags are common ways hackers hide malicious code. 
• Scan the database 
  Download your database and scan it using antivirus software. Malware can sometimes be embedded within the database, and this extra layer of scrutiny can help detect hidden threats. 

3. Proactively defend your website from malware 

Malware attacks are unpredictable. That is why you need to be proactive in monitoring and detecting malware before it can breach the core of your website. 

Here are tools and ways you can build a fortress of safety for your website: 

• Google Search Console (GSC) 
  GSC is a valuable tool for detecting malware infections. Google will alert you if it finds malware or hacked content on your site. Regularly checking this tool can provide early warnings and allow you to address issues quickly. 
• Google Safe Browsing 
  You can use Google Safe Browsing to check whether your site has been flagged as unsafe due to malware. This tool will let you know if Google is warning users about your website’s security. 
• Intrusion Detection Systems (IDS) 
  To continuously monitor your website for suspicious activity, an Intrusion Detection System (IDS) can help. IDS monitors server traffic and sends alerts when it detects unusual patterns that could indicate malware. 
• Behavior monitoring 
  Monitor server and website behavior to spot abnormalities. Unexplained spikes in traffic or data activity can be a sign that malware is at work behind the scenes, sending data to unauthorized locations. 

How to remove malware safely 

Once you detect malware, don’t panic. There are ways to remove it quickly but carefully from your website: 

1. Backup your website 

Before making any changes, always back up your entire website. You’ll never know what may happen during the cleanup. To be on the safe side, always back up your files so you can restore your site if anything goes wrong. 

Here’s how to back up your website effectively: 

• Use your web hosting control panel. Most hosting providers, including Network Solutions, offer an easy way to back up your website through their control panel. Log in to your hosting dashboard and look for options labeled Backup or Backup Wizard. From there, you can create a full backup of your website files and databases. 
• You can manually backup your website files via FTP. Use an FTP client (FileZilla, WinSCP, Transmit for macOS, and Cyberduck) to connect to your web server. Download all your website files, including folders like public_html, and export your website database (usually via phpMyAdmin) to save your content and settings. 
• You can also automatically backup your website through a content management system (CMS) backup plugin. If your website runs on WordPress or another CMS, there are plugins that automate backups. Install a trusted plugin, configure it to back up your files and database regularly, and store backups safely off-site (like cloud storage). 
• Always save your backups in a safe place outside your website server. It can be your local computer, an external drive, or a cloud storage service like Google Drive or Dropbox. 

2. Use malware removal tools 

If you have SiteLock, it offers automatic malware removal services that scan your site, remove infections, and repair affected files. For manual removal, use security plugins or tools compatible with your CMS (like WordPress plugins). 

3. Remove suspicious files and code 

Go through your website files and remove any scripts or files identified as malware. But be cautious. Deleting the wrong files can ruin your site. If you’re unsure, consider professional help. Check your hosting provider if they offer tech support. For Network Solutions, we have MyTime Support™ that can confidently handle technical issues. If you sign up for a Website Support + Whole Office Support plan, you’ll have a trusted and capable expert to deal with removing suspicious files and code. 

4. Update all software and plugins 

Outdated CMS platforms, plugins, and themes are common entry points for malware. After cleanup, update everything to the latest versions to close security gaps. 

5. Change all passwords 

Reset your website’s admin, FTP, database, and hosting passwords. Use strong, unique passwords to prevent hackers from getting back in. 

6. Run a full scan again 

After cleanup, run a fresh scan with SiteLock or your chosen tool to confirm your site is clean. Repeat scans regularly to stay safe. 

Protect your website from malware infections 

Prevention is always better than cure. Here’s how Network Solutions helps you keep your site protected: 

• SiteLock secure hosting provides built-in malware scanning and removal, plus firewall protection to block threats before they reach your site. 
• SSL certificates encrypt data between your site and visitors, preventing attackers from intercepting information or injecting malware. 
• Website backup services let you restore your site quickly if malware strikes, minimizing downtime and loss. 

Prevent malware: Best practices for ongoing protection 

Protecting your website from malware isn’t just about tools—it’s also about building smart habits that make your site a hard target for hackers. 

Here’s how you can strengthen your website’s defenses: 

Keep everything updated 

Hackers often exploit vulnerabilities in outdated software. Make it a habit to regularly update your website’s CMS, plugins, themes, and server software. Many CMS platforms like WordPress allow you to enable automatic updates, which helps ensure you never miss critical security patches. 

Tip: Schedule monthly checks to review updates and install them promptly. If you use custom plugins or themes, check with developers about updates regularly. 

Limit admin access 

Only grant website admin or backend access to trusted team members who absolutely need it. Each additional user with admin rights increases the risk of credentials being leaked or misused. Use role-based permissions to give users only the access they need. For example, editors or contributors instead of full admins. 

Tip: Regularly review your user list and remove access for people who no longer work on the site or need permissions. 

Use strong passwords and two-factor authentication (2FA) 

Weak passwords are one of the easiest ways for attackers to break into your website. Make sure all admin and FTP passwords are complex, unique, and changed regularly. Two-factor authentication adds a second layer of protection by requiring a code from your phone or email to log in. 

Avoid installing suspicious plugins or themes 

Plugins and themes from unofficial or unknown sources can contain malicious code that infects your website. Always download and install plugins from trusted repositories such as the official WordPress plugin directory or reputable vendors. 

Tip: Before installing, check reviews, last update dates, and support responsiveness to ensure the plugin or theme is well-maintained. 

Regularly monitor your site’s health 

Use security tools to scan your site daily for malware, vulnerabilities, and suspicious activity. Your hosting provider may also offer monitoring features or alerts to notify you of any unusual behavior. 

Tip: Set up automated alerts so you can respond quickly if your website’s security is compromised. 

Educate your team 

Your website’s security is only as strong as the people who manage it. Train your team on basic security principles, such as recognizing phishing emails, avoiding suspicious downloads, and following password best practices. This reduces the chance of accidental breaches caused by human error. 

Tip: Hold quarterly security refresher sessions and share simple security checklists with your team. 

Keep malware out and customers in 

Malware isn’t just an IT problem — it threatens your customers’ trust and your whole business. Learning how to detect malware early and remove it effectively helps you keep your site running smoothly and securely.  

That is why a reliable partner offering automated malware detection, removal, and ongoing protection tailored for small to medium businesses is what you need. Network Solutions is the partner you need.  

Network Solutions offer domain registration, robust website builders, website hosting, and trusted security services. We have SiteLock to protect you from website and SSL certificates to protect your business reputation. 

Protect your business today with Network Solutions so you can focus on growing your business with confidence. 

Frequently asked questions