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How to Detect and Remove Malware from Your Website

By James Tredwell on March 25, 2025

Everything was working smoothly on your website until now, but today it started behaving strangely; it has become a bunch of errors, started slowing down and redirecting visitors unexpectedly—showing unnecessary ads and pop-ups or getting blocked by search engines due to safety concerns. Malware can quietly penetrate your website and turn it into a security nightmare, impacting performance, brand identity, and customer loyalty. But the good news is that you can identify and delete these threats before they do lasting harm.

This blog will help you learn how to identify and effectively remove malware. Whether you rely on an SSD hosting provider or are looking for the cheapest Linux server hosting, website security is a must. So, are you ready to secure your website? Let’s go..

Warning Signs of Hidden Malware

Some malware attacks are usually detected almost immediately; the most untrained eye can spot website defacements. Defacement occurs when hackers manipulate your existing website content with their own message or image. While indeed a small percentage of all malware attacks are defacements, even hidden malware may leave traces of its work that could be detected by either the website owner, visitors, or both.

Of course, other signs of a malware-infected website include improper alternations of your user account logins, missing or changed website files, web pages freezing or crashing, or a significant drop in traffic. Additionally, if your hosting company detects this malware, a notification could reach you regarding the same, and it might result in an account suspension. Furthermore, search engines might even “blacklist” your website in case the evidence for such malware is certain.

The signs of an attack are never a good thing—particularly for small business owners. The consequences of a malware attack can involve long-term damage to search rankings, website usability, and more. If your website is blacklisted or suspended, it will do the very opposite of stimulating customer confidence and restoring reputation and could even serve to actively reduce revenues.

Cleaning Up Malware to Restore Your Website’s Security

The degree of damage done by a malware attack on a website is generally influenced by several factors; the response time is one of the most important of them. The longer it takes to detect and eliminate the malware, the more expensive the recovery will be. Unfortunately, a lot of malware is deliberately written to be low-key for as long as possible. Eventually, however, the signs of a malware-infected website will be hard to ignore.

Those who don’t have any tech skills probably find it best to let a security specialist handle the cleaning. You can use a website malware scanner that scans your website every single day and removes malware automatically upon detection. Developers or any other tech-savvy people may as well choose to manually remove the malware themselves, given the time and resources.

If you choose to remove the malware manually, here’s what you need to do:

1. Find Out the Source

You may do it through a file manager or through a local file search or command line. Most web hosts provide file managers, which are generally optimized for basic file modification rather than specific content searches.

A local search, as it implies, gets the contents of your live website downloaded on your local machine, so the searching is a little less cumbersome than it is otherwise. Access to the command line is rare in a shared hosting scenario, but if you have it, you can search for much more detail. With it, you can find files recently modified and certain contents within files.

2. Look For the Perfect Clues

When you have identified the files that you suspect have been infected, you must try to find common syntax used by the attackers to inject the website with malware. Look through these PHP code snippets: eval, base64_decode, fromCharCode, gzinflate, shell_exec, globals, and error_reporting(). These are merely a drop in the bucket in terms of modern functions used by cybercriminals, but each appears in many of the PHP hacks.

3. Delete the Harmful Software

Once the offending files are identified, remove them, and your website will be cleared of malware. Although manual deletion of the malware can be undertaken, we always advise a website scanner for faster and more accurate results. SiteLock is an example of a scanner that automates the detection of malware and its remediation. It works by subjecting the website to a file transfer protocol scan to download, inspect, and clean those website files and then upload them back to the host server behind the scenes with no interruption of user experience.

Conclusion: Security Problems with Websites Never Go Away

Every website owner knows that defending against malware requires an endless effort. When trying to minimize the risk, the focus must be placed on preventing the vulnerabilities in your website’s source code because cybercriminals are definitely going to try to backdoor this method. This is achievable even for the non-tech-savvy person, i.e., if you don’t know programming, just apply your updates and patches as soon as they come in. An even better solution is to use an automated patching system. The same goes for plugins and features: keep only what you need and delete the ones you never use.

Automated vulnerability scanners are used to scan for areas of improvement and should never be confused with malware scanners. Ideally, the one you use for website monitoring with a CMS such as WordPress or Drupal will include a vulnerability scanner that automatically patches vulnerabilities. Antivirus or malware scanners relate to detecting viruses, trojans, ransomware, and other forms of malware on the device while providing solutions in real-time. Last but not least, have a web application firewall in place to protect against malicious bot activities, which cybercriminals use in search of possible entry points.

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