How to Perform a Clean Boot in Windows 11: Step-by-Step Guide

By / September 24, 2025

Summary (Key Takeaways)

  • A clean boot starts Windows 11 with only essential services and drivers.

  • It helps you diagnose software conflicts, crashes, or performance issues.

  • You can do it using System Configuration (msconfig) and Task Manager.

  • Clean boot ≠ Safe Mode → Clean boot loads Windows normally but disables third-party services.

  • This guide provides a step-by-step process with pro tips and troubleshooting advice.

Have you ever faced random freezes, app crashes, or error messages in Windows 11 that just won’t go away? The culprit is often a software conflict — when two programs or services clash.

One of the best ways to troubleshoot is by performing a clean boot. Unlike Safe Mode, a clean boot loads Windows normally, but disables all non-Microsoft services and startup apps.

In this guide, you’ll learn exactly how to perform a clean boot in Windows 11 step by step, why it’s useful, and how to undo it once you’ve identified the problem.

What Is a Clean Boot in Windows 11?

A clean boot is a troubleshooting method where Windows starts with:

  • Only essential Microsoft services

  • No third-party startup apps

This environment makes it easier to check if the issue is caused by software conflicts (like antivirus, drivers, or background programs).

When Should You Perform a Clean Boot?

  • Windows is slow to boot or freezes randomly

  • Apps or games crash on launch

  • Windows Update fails repeatedly

  • Strange error messages keep appearing

  • To troubleshoot driver conflicts

👉 If Windows works fine in clean boot mode, the issue is likely caused by third-party software.

Clean Boot vs. Safe Mode: What’s the Difference?

Feature Clean Boot Safe Mode
Startup Apps Disabled Disabled
Non-Microsoft Services Disabled Disabled
Drivers Loaded Normal drivers Minimal drivers only
Use Case Troubleshoot software conflicts Troubleshoot system/driver issues

How to Perform a Clean Boot in Windows 11 (Step-by-Step)

Step 1: Open System Configuration

  1. Press Win + R to open the Run dialog.

  2. Type:

    msconfig

  3. Press Enter.

Step 2: Configure Services

  1. In the System Configuration window, go to the Services tab.

  2. Check Hide all Microsoft services (important — don’t disable system-critical services).

  3. Click Disable all.

  4. Click Apply.

Step 3: Disable Startup Programs

  1. Go to the Startup tab in System Configuration.

  2. Click Open Task Manager.

  3. In Task Manager, under the Startup tab, right-click each third-party app and select Disable.

Step 4: Restart Your PC

  • Close all windows and restart.

  • Windows 11 will now boot in clean boot mode with only essential services running.

How to Identify the Problem in Clean Boot

Now that your PC is running in clean boot:

  1. Use Windows normally.

  2. If the issue is gone → it’s caused by a disabled service or startup app.

  3. To find the culprit:

    • Re-enable services and startup apps one by one.

    • Restart after each change.

    • When the issue reappears, the last program enabled is the cause.

How to Exit Clean Boot in Windows 11

Once you’re done troubleshooting, restore normal startup:

  1. Press Win + R, type msconfig, and press Enter.

  2. Under General, select Normal startup.

  3. Go to the Services tab → click Enable all.

  4. Go to Task Manager > Startup tab → re-enable necessary apps.

  5. Restart your PC.

Pro Tips for Clean Boot Troubleshooting

  • Always note down which services you disable to avoid confusion.

  • If multiple apps are suspicious, enable them in groups to save time.

  • Avoid disabling antivirus or firewall until you’re sure they’re the cause.

  • If you find the faulty app, consider updating or reinstalling it instead of leaving it disabled.

Common Problems and Fixes

❓ Clean boot didn’t fix my issue

  • Try Safe Mode instead — the problem may be driver-related.

❓ I accidentally disabled a Microsoft service

  • Go back into msconfig → uncheck “Hide all Microsoft services” → re-enable.

❓ My PC is still slow after clean boot

  • The issue may be hardware-related (e.g., failing HDD/SSD, low RAM).

Conclusion

Performing a clean boot in Windows 11 is one of the most effective ways to diagnose software conflicts. By disabling third-party services and apps, you can quickly determine whether the issue lies in Windows itself or in external programs.

  • Use System Configuration + Task Manager to set up the clean boot.

  • Test your system.

  • Re-enable services/apps gradually to pinpoint the cause.

  • Return to normal startup once troubleshooting is done.

This simple process can save hours of frustration and help you maintain a stable, smooth Windows 11 experience.

FAQs

1. What does a clean boot do in Windows 11?

It starts Windows with only essential services and drivers, helping troubleshoot software conflicts.

2. Is clean boot the same as Safe Mode?

No. Clean boot loads Windows normally but without third-party apps. Safe Mode loads with minimal drivers and a stripped-down UI.

3. Will a clean boot delete my files?

No. It only disables apps and services temporarily — your files remain safe.

4. How long should I keep my PC in clean boot mode?

Only as long as needed for troubleshooting. After finding the culprit, return to normal startup.

5. Can I perform a clean boot on Windows 11 Home edition?

Yes. The msconfig method works on all Windows 11 editions, including Home.

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