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How to Install, Configure, and Run a Deep Malwarebytes Scan on Windows

Malwarebytes is a helpful tool for checking a Windows computer for malware, unwanted programs, suspicious files, and other threats. The free version can be used as an on-demand scanner, meaning you can install it, run a scan when needed, and review anything it finds.

This guide walks you through downloading Malwarebytes, installing it, enabling rootkit scanning, and running a deeper custom scan across your drives.

Malwarebytes’ current Windows scan settings allow users to customize Threat Scans and Custom Scans, including options such as quarantine behavior, restart behavior, and custom scan preferences.

1. Download Malwarebytes

Go to the official Malwarebytes download page:

Malwarebytes Free Download:
https://www.malwarebytes.com/mwb-download

Click the Free Download button and save the installer to your computer.

2. Open the Installer

After the download finishes:

  1. Open your Downloads folder.
  2. Locate the Malwarebytes installer file.
  3. Double-click the file to begin installation.
  4. Follow the on-screen prompts.

When Malwarebytes asks how you plan to use the software, choose Personal.

3. Skip Optional Add-ons if You Only Want the Free Scanner

During setup, Malwarebytes may offer a premium trial, browser extensions, or additional protection features.

If your goal is only to use Malwarebytes as a free on-demand scanner, you can skip the premium trial and browser extensions.

The free scanner is useful when you want to manually check a system, but it is not the same as full-time managed protection.

4. Enable Rootkit Scanning

By default, standard Malwarebytes Threat Scans may not check for rootkits unless the option is enabled.

Rootkits are deeper-level threats that can hide inside the operating system. Scanning for them can take longer, but it is a good option when you want a more thorough check. Malwarebytes forum guidance notes that enabling rootkit scanning can make scans take longer because it performs lower-level disk and file analysis.

To enable rootkit scanning:

  1. Open the Malwarebytes application.
  2. Click the Gear icon for Settings, usually located near the top-right of the dashboard.
  3. Go to the Security tab.
  4. Scroll down until you find Scan for rootkits.
  5. Switch the toggle to On.

5. Start a Custom Scan

For the most complete manual scan, run a Custom Scan instead of only using the basic scan option.

To start a Custom Scan:

  1. Return to the main Malwarebytes dashboard.
  2. Click Scanner.
  3. Choose Advanced Scan or Custom Scan, depending on the version of Malwarebytes you are using.
  4. Select Configure Scan.

A custom scan allows you to choose specific drives, folders, and scan options. Malwarebytes support documentation confirms that Malwarebytes for Windows supports configurable custom scans.

6. Select All Drives and Scan Options

Inside the custom scan configuration screen:

  1. Check all available drives, such as:
    • C:
    • D:
    • Any external drives you want scanned
  2. Make sure Scan for rootkits is checked in the custom scan options.
  3. Review any other scan options shown on the screen.
  4. Click Scan to begin.

A custom scan can take a long time, especially when scanning multiple drives, large file collections, or external storage. That is normal.

7. Review the Results

When the scan finishes, Malwarebytes will show the results.

If threats are found:

  1. Review the listed items.
  2. Leave suspicious items selected unless you know they are safe.
  3. Click Quarantine.
  4. Restart the computer if Malwarebytes recommends it.

If no threats are found, you can close the results screen.

Cloud Fixer Recommendation

For normal users, Malwarebytes is a good second-opinion scanner when a computer is acting strange, showing pop-ups, running slowly, or possibly infected.

For business systems, medical offices, servers, or computers with sensitive data, do not rely on a single malware scan as your full security plan. You should also review antivirus status, Windows updates, browser extensions, startup items, backups, user accounts, remote access tools, and suspicious sign-ins.

Need help checking a system? Cloud Fixer can help review the computer, scan for threats, clean up suspicious software, and make sure your security tools are configured correctly.

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