Some links on this page are affiliate links: if you buy through them we may earn a commission, at no extra cost to you.
To run Malwarebytes’ most comprehensive Windows scan, open the app and select the three-dot menu beside Scan—not the main Scan button. Choose Advanced Scan, then Deep Scan. Malwarebytes recommends Deep Scan mainly as a follow-up after malware has been blocked or detected, rather than as your everyday scan.
Before you start
Deep Scan uses more system resources than a routine scan and may slow Windows for an extended period. Before starting:
- Save open documents and other work.
- Plug in a laptop.
- Close demanding or disk-intensive applications if possible.
- Allow extra time for the scan to finish. Malwarebytes does not provide a guaranteed duration, because scan time varies with storage capacity, file count, drive speed, and system activity.
- Install any Malwarebytes application or protection-database update offered by the app.
These are practical precautions, not a fixed Malwarebytes requirement. The current Malwarebytes instructions warn that Deep Scan can affect performance and take longer than other scan types.
Do these 3 things before closing this tab:
1Repair Windows errors before they cause bigger problems2Fix the driver behind crashes, sound loss and screen glitches3Clear out junk files and repair common Windows errorsHow to start a Deep Scan
- Open Malwarebytes for Windows.
- On the dashboard, locate the Scan button.
- Click the vertical three-dot menu beside Scan.
- Select Advanced Scan.
- Select Deep Scan. The scan starts automatically.
- Wait for the scan to complete.
- Reopen Malwarebytes when finished, review the scan report, and quarantine detected threats.
Important: Clicking the main Scan button launches a Threat Scan, not a Deep Scan. The current menu path is Malwarebytes dashboard → three dots beside Scan → Advanced Scan → Deep Scan. See Malwarebytes’ current Deep Scan instructions.
#1 Best Overall
- SPEED-OPTIMIZED, CROSS-PLATFORM PROTECTION: World-class antivirus security and cyber protection for Windows (Windows 7 with Service Pack 1, Windows 8, Windows 8.1, Windows 10, and Windows 11), Mac OS (Yosemite 10.10 or later), iOS (11.2 or later), and Android (5.0 or later). Organize and keep your digital life safe from hackers
- SAFE ONLINE BANKING: A unique, dedicated browser secures your online transactions; Our Total Security product also includes 200MB per day of our new and improved Bitdefender VPN
- ADVANCED THREAT DEFENSE: Real-Time Data Protection, Multi-Layer Malware and Ransomware Protection, Social Network Protection, Game/Movie/Work Modes, Microphone Monitor, Webcam Protection, Anti-Tracker, Phishing, Fraud, and Spam Protection, File Shredder, Parental Controls, and more
- ECO-FRIENDLY PACKAGING: Your product-specific code is printed on a card and shipped inside a protective cardboard sleeve. Simply open packaging and scratch off security ink on the card to reveal your activation code. No more bulky box or hard-to-recycle discs. PLEASE NOTE: Product packaging may vary from the images shown, however the product is the same.
What Deep Scan does
Malwarebytes describes Deep Scan as a comprehensive scan that uses advanced detection techniques and a broad malware database to check system locations for threats. It is more thorough than the routine Threat Scan, but the documentation does not say that it examines every byte or every file on the computer. Avoid treating “Deep” as a guarantee of total coverage.
Deep Scan is especially appropriate when:
- Malwarebytes or another security product detected malware.
- Malwarebytes blocked a threat and you want a more complete follow-up check.
- Symptoms continue after an initial detection or removal.
- You suspect that an infection left additional components behind.
For ordinary recurring checks, Malwarebytes recommends using Threat Scan rather than running Deep Scan every time. Its scan-type guide explains the differences between the available options.
Deep Scan compared with other Malwarebytes scans
| Scan | Best use | How it differs |
|---|---|---|
| Threat Scan | Routine checking | Searches common system locations. Paid subscriptions schedule it weekly by default. |
| Quick Scan | A fast check | Checks memory and startup programs and is less comprehensive than Threat Scan. Malwarebytes says Quick Scan on Windows is available only to paid subscribers. |
| Custom Scan | Specific files, folders, or drives | Lets you choose what to scan. Selecting many locations can make it lengthy. |
| Deep Scan | Follow-up after malware detection or blocking | Uses advanced detection techniques, checks more comprehensively, and can have a longer performance impact. |
Malwarebytes lists these scan types for Windows and macOS, although Deep Scan is listed as a Windows scan. Availability can depend on the installed product, account, subscription, application version, and current interface. The current Deep Scan instructions do not state that it is universally free or universally paid.
When the scan finishes
Malwarebytes says its app icon flashes in the Windows system tray when the scan is complete. Open Malwarebytes and inspect the scan report before deciding what to do.
Rank #2
![Norton 360 Deluxe Antivirus, 5 Devices, Auto-Renews [Download]](https://m.media-amazon.com/images/I/41IYV5zGyCL._SL160_.jpg)
- ONGOING PROTECTION Download instantly & install protection for 5 PCs, Macs, iOS or Android devices in minutes!
- TOP-PERFORMING VPN Faster speeds, more server locations, and greater connection control to protect your privacy across all your devices, including Smart TVs.
- ADVANCED SCAM PROTECTION Help spot hidden scams online. With the built-in Genie AI assistant, you’ll never wonder if a message or email is suspicious again.
- REAL-TIME PROTECTION Advanced security protects against existing and emerging malware threats, including ransomware and viruses, and it won’t slow down your device performance.
- DARK WEB MONITORING Identity thieves can buy or sell your information on websites and forums. We search the dark web and notify you should your information be found.
- Review each detection’s name and file path.
- Use Malwarebytes’ quarantine action for detections unless you have a specific reason to investigate one first.
- Restart Windows if Malwarebytes or Windows requests it.
- Run another appropriate scan if symptoms remain.
- Preserve or export the report if you need Malwarebytes support.
Do not restore a quarantined item merely because you recognize its filename. Legitimate software can be bundled with potentially unwanted programs, and malware can use familiar names.
If Deep Scan is missing
Do not assume immediately that the feature has been removed or that you must reinstall the software. Work through this sequence:
- Confirm that you opened Malwarebytes for Windows—not a browser extension, mobile app, or another Malwarebytes product.
- Look specifically for the three-dot menu beside Scan.
- Update Malwarebytes, then close and reopen the app.
- Check the installed product, account, and subscription status.
- Use Threat Scan or Custom Scan as an interim option.
- Contact Malwarebytes support if the documented menu remains absent.
Labels may differ between product editions, older builds, Windows versions, and staged interface changes. The obsolete “Desktop Security” wording may also appear in older links or documentation; Malwarebytes’ current page is titled Run a Deep Scan in Malwarebytes for Windows and was updated June 30, 2026.
If Deep Scan appears stuck
The current Malwarebytes article does not provide a specific stuck-scan recovery procedure. As practical troubleshooting:
Rank #3
![Norton 360 Premium Antivirus, 10 Devices, Auto-Renews [Download]](https://m.media-amazon.com/images/I/41JNWru8mYL._SL160_.jpg)
- ONGOING PROTECTION Download instantly & install protection for 10 PCs, Macs, iOS or Android devices in minutes!
- TOP-PERFORMING VPN Faster speeds, more server locations, and greater connection control to protect your privacy across all your devices, including Smart TVs.
- ADVANCED SCAM PROTECTION Help spot hidden scams online. With the built-in Genie AI assistant, you’ll never wonder if a message or email is suspicious again.
- REAL-TIME PROTECTION Advanced security protects against existing and emerging malware threats, including ransomware and viruses, and it won’t slow down your device performance.
- DARK WEB MONITORING Identity thieves can buy or sell your information on websites and forums. We search the dark web and notify you should your information be found.
- Wait before cancelling if disk activity is still visible.
- Open Windows Task Manager and check Malwarebytes’ CPU, memory, and disk activity.
- Close other applications that are heavily using the disk.
- If Windows becomes unusable, save work if possible, cancel the scan, restart Malwarebytes, and try again.
- Record the visible error, stopping point, scan report, and Malwarebytes version before contacting support.
If the computer appears actively compromised, disconnect it from networks where appropriate and consider a trusted second-opinion or offline scan.
If Malwarebytes detects malware
Quarantine the detection through Malwarebytes rather than manually deleting files. Afterward, restart if requested and run another suitable scan if symptoms continue. Depending on the detection, also review browser extensions, startup items, recently installed applications, scheduled tasks, and account-security activity for signs of persistence.
If credentials may have been exposed, change important passwords from a clean device. Enable multifactor authentication where available. Keep the scan report for support or further investigation.
Free tools Windows power users keep installed
One-click scans. No signup required.
Malwarebytes Deep Scan versus Microsoft Defender Offline
Deep Scan runs inside normal Windows. Microsoft Defender also provides Full and Custom scans through Windows Security, plus Microsoft Defender Offline. Offline scanning restarts the computer and scans from the Windows Recovery Environment before the usual Windows environment loads. That makes it useful when malware may be persistent, normal Windows appears compromised, or an in-Windows scan cannot remove the threat. Results appear in Protection history.
Rank #4
- DEVICE SECURITY - Award-winning McAfee antivirus, real-time threat protection, protects your data, phones, laptops, and tablets
- SCAM DETECTOR - We'll automatically identify risky texts, emails, and videos that attempt to steal your personal or financial information. You can even use our mobile app to check social messages and QR codes for scams on-demand, without missing a beat.
- SECURE VPN – Secure and private browsing, unlimited VPN, privacy on public Wi-Fi, protects your personal info, fast and reliable connections
- IDENTITY MONITORING – 24/7 monitoring and alerts, monitors the dark web, scans up to 60 types of personal and financial info
- SAFE BROWSING – Guides you away from risky links, blocks phishing and risky sites, protects your devices from malware
To access Microsoft’s scan options, open Windows Security → Virus & threat protection → Scan options. Save your work before selecting Defender Offline because it restarts the PC. Microsoft’s documentation covers supported Windows 10 and Windows 11 installations; see Microsoft’s Virus and threat protection guide.
Defender Offline is an escalation option, not proof that Malwarebytes Deep Scan is inadequate. The two products use different scan modes and detection systems, so choose based on the situation rather than assuming one is universally better. Do not routinely disable Microsoft Defender before running Malwarebytes.
Independent reader supportYour contribution helps us test, update, and keep practical guides available for everyone.Free scan or ongoing protection?
If you need a one-time or occasional second-opinion scan, Malwarebytes’ free tools are the relevant starting point. Ongoing real-time protection is a separate product decision; Malwarebytes describes Premium as adding continuous protection features. Deep Scan availability should be determined from the options shown in your installed app and account—not from an assumption about the free or paid edition.
A clean Deep Scan is reassuring, but no scanner can guarantee that a computer is perfectly safe. Persistent symptoms may have non-malware causes or may require offline scanning, software updates, account protection, or professional assistance.
Best Value
- POWERFUL, LIGHTNING-FAST ANTIVIRUS: Protects your computer from viruses and malware through the cloud; Webroot scans faster, uses fewer system resources and safeguards your devices in real-time by identifying and blocking new threats
- IDENTITY THEFT PROTECTION: Protects your usernames, account numbers and other personal information against keyloggers, spyware and other online threats targeting valuable personal data
- REAL-TIME ANTI-PHISHING: Proactively scans websites, emails and other communications and warns you of potential danger before you click to effectively stop malicious attempts to steal your personal information
- ALWAYS UP TO DATE: Webroot scours 95% of the Internet three times per day including billions of web pages, files and apps to determine what is safe online and enhances the software automatically without time-consuming updates
Frequently Asked Questions
Does Deep Scan scan every file on the PC?
Malwarebytes describes it as a comprehensive scan of system locations using advanced detection techniques. Its current documentation does not promise that every file or every byte is examined.
How long does a Deep Scan take?
There is no fixed official duration. The time depends on factors such as storage size, file count, drive speed, and system activity.
Can I use the PC while Deep Scan runs?
You can, but performance may be affected. Save your work and avoid demanding applications while the scan is running.
Quick wins for a faster PC:
Repair Windows errors before they cause bigger problemsFix Now →Scan for outdated or missing drivers - takes under a minuteDriver Scan →Clear out junk files and repair common Windows errorsFree Scan →Is Deep Scan included in the free version?
The current Deep Scan instructions do not state a universal free-or-paid rule. Check the scan options shown in your Malwarebytes product and account.
Should I run Defender Offline too?
Consider it when malware appears persistent, Windows seems compromised, or a normal scan cannot remove the threat. It restarts the computer, so save work first.
Quick Recap
Product prices and availability are accurate as of the date/time indicated and are subject to change. Any price and availability information displayed on Amazon at the time of purchase will apply.
