How to disinfect Windows with Malwarebytes step by step

If your PC with Windows has become slow, pop-ups appear or you notice strange behavior, it's time to take action with a complete disinfection with Malwarebytes and advanced cleaning techniques. In this handy, organized guide, I explain how to remove malware step by step, from the basics to the most sophisticated, including rootkits, hidden startup entries, and system issues. Boot.

Before we begin, a key clarification: malware and viruses are not synonymous; a virus is just one type of malware within a spectrum that includes Trojans, worms, adware, ransomware, spyware, rootkits, and more. Knowing this difference helps you choose better tools and methods, and understand why sometimes it takes more than a quick scan to get your system spotless.

What is Malwarebytes and why is it useful on Windows?

Malwarebytes is a powerful anti-malware software (not a traditional antivirus) designed to detect and remove modern threats that many legacy engines miss. It offers a Premium trial period of approximately 14-15 days, and after the trial period, you can continue using its on-demand scans to clean already infected systems.

Its Premium edition includes several layers of real-time, web, ransomware, exploit, and malware protection, as well as specific controls for PUPs (potentially unwanted programs) and PUMs (potentially unwanted modifications). These layers cut dangerous connections, prevent malicious executions y They quarantine threats preemptively.

Be careful with the nuance, Malwarebytes is not intended to replace a complete antivirus, and is perfectly compatible with Windows Defender if you want a layered strategy. In fact, its value lies both in proactive protection and post-infection cleanup, an area where it particularly shines.

To put its real effectiveness into context, there are testimonials from satisfied users that support its usefulness in complicated cleanings (for example, cases such as Robin G. in Fort Worth, TX; Billy H. in Sarasota, FL; or Raymond P. in Southfield, MI). It's a versatile tool for both occasional use and keeping it resident, adjusting the shields if you need to optimize resources.

Essential preparations before disinfecting

1. Disconnect your computer from the Internet as soon as you suspect an infection to cut off communication with potential command and control (C&C) servers and prevent network spread. This step reduces the risk of data theft and prevents lateral movement of malware.
2. Whenever possible, boot Windows into Safe Mode (with or without networking, depending on your needs) to limit the load on drivers and services, thus minimizing malware interference during cleanup. For many infections, this environment facilitates removal without blockages.
3. Rebooting occasionally helps clear RAM of ephemeral processes, but it doesn't remove persistent malware from your disk, so consider it a backup, not a permanent solution. After the restart, resume the disinfection plan.
4. Back up your important data to a disconnected storage medium and, if possible, verify that there are no infected files on that backup to prevent re-infections later. Prioritize documents, photos, and irreplaceable materials, not executables or dubious installers.

Install and update Malwarebytes on Windows

Download Malwarebytes from its official website, run the installer, choose the language and path, and complete the installation in just a few clicks; it's a quick and hassle-free process. The Premium trial is activated automatically so you have full protection for the first few days.

As soon as you open it, check for program and software updates. databases of threats, forcing the search if the computer has not been connected for a long time or if there was a previous update failure. Having up-to-date signatures and components makes the difference in detection.

In Settings, you can control how often threat intelligence updates are updated (from every 15 minutes to 14 days), whether you want updates to be automatic, and which components are updated together. My recommendation: leave it on automatic and with frequent intervals for maximum coverage.

Explore the General, Security, Notifications, and Display sections to customize behavior, language, and programming of analysis and how you want the notifications and interface to be displayed. A quick glance at these tabs will save you time later.

Real-time protection and how it works

Web protection monitors your browser's input and output and cuts off connections to malicious or phishing sites, acting as a reputation firewall to prevent dangerous payloads. It is a very effective shield against malvertising, downloads silent and impersonations.

Anti-malware, anti-ransomware, and anti-exploit protections prevent suspicious files from running (even from pen drive), blocking typical malicious encryption behaviors and neutralizing attempts to exploit vulnerabilities. If something is detected, is sent to quarantine y you decide the final destination.

Quarantine isolates detected items so they can't be executed without immediately deleting them, giving you time to review potential false positives and restore them if necessary. It is a safe and reversible approach until you confirm permanent removal.

Typical case: Activation tools or "hacktools" can be classified as riskware by their nature; they don't always contain malicious code, but they pose legal and security risks. If you don't need them, it's wise to delete them to avoid leaving back doors.

Types of scans with Malwarebytes

Fast, intelligent threat analysis is ideal for everyday use, scanning critical memory, registry, boot, and other locations where malware often hides. It is the one that should be programmed automatically to maintain system hygiene.

Scheduled scanning is opportunistic: if it can't be started at the scheduled time, Malwarebytes will try again later that day to ensure you don't miss a single snag in your protection. Adjust the frequency to your actual equipment usage.

Custom scanning adds depth: you can include rootkit scanning, scanning inside compressed files, inspecting memory objects, the Windows Registry, and startup programs. Use when you suspect persistent infection or after serious incidents.

Configure PUP/PUM handling (block, recommend, or ignore) and define exclusions for routes you know cause false positives, always judiciously and only if strictly necessary. Fewer exclusions means less risk surface.

Step-by-step disinfection with Malwarebytes

1. Disconnect the internet to prevent malware from communicating and spreading on your local network. This cutoff is critical when you suspect C&C Trojans.
2. Start Windows in Safe Mode with Networking only if you're updating signatures; if you've already updated, regular Safe Mode further reduces the attack surface. This will prevent malware from loading and blocking cleanup.
3. Run a threat scan with Malwarebytes and, upon completion, quarantine everything detected unless you positively identify a false positive. Do not run or open anything during the scan.
4. Restart when prompted to complete pending actions, then perform a second scan to detect remnants of attempted restoration. Double pass increases the overall removal rate.
5. Optional but useful: Clear your browser and system cache; this will rarely be the source of the problem, but it helps prevent poisoned web content stored locally from running. Also take the opportunity to update your browser and extensions.
6. Change passwords for your critical accounts (email, banking, social media) from a clean device and check login activity; some infections steal credentials. Enable 2FA when available.

When malware doesn't fall the first time: advanced techniques

There are threats (rootkits, bootkits, polymorphic or zero-day malware) that camouflage themselves at deep levels and require additional tools and methods beyond standard Malwarebytes. In these cases, it combines specialized scanners and forensic utilities such as ComboFix.

Inspects processes with the Task Manager And if you see anything strange, go to Microsoft Process Explorer to check the digital signature, paths, loaded modules, and behavior. A process without a trusted editor on a suspicious path is a bad sign.

Scan for rootkits with utilities like Malwarebytes Anti-Rootkit or TDSSKiller; GMER is very powerful but is not currently supported. Windows 11. Run these tools preferably in Safe Mode for maximum effectiveness.

Check the startup with Autoruns and clean up any entries you don't recognize; also validate the startup registry keys in HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Run. Disable first and remove after confirming that everything is stable; also validate the shortcuts (.lnk) that start programs automatically.

Monitor suspicious connections: With netstat -ano you can view associated ports and processes, and with Wireshark you can capture traffic to identify anomalous remote IPs. If you detect data exfiltration, shut down the internet and prioritize containment.

Related article:

Complete tutorial to disinfect your device with Malwarebytes

Isaac

Passionate writer about the world of bytes and technology in general. I love sharing my knowledge through writing, and that's what I'll do on this blog, show you all the most interesting things about gadgets, software, hardware, tech trends, and more. My goal is to help you navigate the digital world in a simple and entertaining way.