How to Perform a Clean Boot in Windows 11 and 10 to Fix Software Conflicts

A clean boot starts Windows with a minimal set of drivers and startup programs, so you can see whether a background app or service is causing the problem. It is one of the most useful troubleshooting steps when you’re trying to track down mysterious performance or stability issues. If your Windows 11 or Windows 10 PC is crashing,  freezing, or running very slowly, it could be due to a software conflict such as a faulty driver, background service, antivirus, or startup program. In such situations, performing a Clean Boot in Windows 11 or 10 helps you identify which application or program is causing the issue so you can troubleshoot accordingly.

This article explains:

• What a clean boot is (and how it differs from Safe Mode)
• What a clean boot does and does not do
• How to perform a clean boot in Windows 11 and Windows 10
• How to use clean boot to find the problematic app or service
• How to return Windows to normal startup after troubleshooting

Note: A clean boot does not delete your files or uninstall your programs. It only disables non‑Microsoft services and startup apps temporarily for troubleshooting.

What Is a Clean Boot in Windows?

A clean boot is a way to start Windows with only a minimal set of drivers and startup programs. When you perform a clean boot:

• All Microsoft services (core Windows services) are left enabled.
• Most third‑party services (from apps you installed) are disabled.
• Startup programs that normally start with Windows are disabled.

This helps you determine whether a background program, driver, or service you installed is causing issues such as:

• Random freezes or slow performance
• Blue screen errors (BSOD) related to drivers or software
• Problems installing or updating programs or Windows itself
• High CPU, RAM, or disk usage caused by third‑party apps

A clean boot is temporary and reversible. After you finish troubleshooting, you can easily return to normal startup.

When Should You Use a Clean Boot in Windows 11 and 10?

Use a clean boot when Windows starts normally, but something is clearly wrong and you suspect a software conflict. For example:

• Your PC crashes or freezes randomly, even after checking for malware.
• You see blue screen errors (BSOD) that might be caused by drivers or third-party programs.
• Apps or games won’t open, or close immediately after you start them.
• Certain tasks (installing programs, running updates, launching games) only fail when other software is running in the background.
• You recently installed new software (antivirus, backup tools, system tweakers, drivers) and problems started afterwards.

In these cases, a clean boot helps you check whether a non-Microsoft service or startup program is causing the issue. If the problem disappears in a clean boot state, you know that something you installed is the likely cause.

If Windows cannot boot at all, or crashes before the desktop appears, a clean boot is not enough use Safe Mode or recovery options instead.

Clean Boot vs Safe Mode – What’s the Difference?

Sometimes you may confuse clean boot with Safe Mode, but they are not the same.

A clean boot provides more control over which services and apps run than Safe Mode.

Safe Mode:

Windows Safe Mode boots only the components required to start Windows and runs with the most stable available driver.

• Loads a minimal Windows environment with a very limited set of drivers.
• Often uses a basic display driver and minimal networking (or none).
• Is designed to help when Windows cannot start normally or when drivers are severely broken.

Clean Boot:

A clean boot does not affect the Windows environment and only removes third-party vendor add-ons that are loaded at startup

• Start Windows normally with your regular display driver and most core features enabled.
• Disables third‑party services and startup programs to isolate software conflicts.
• Is best used when Windows can boot, but you suspect a background app or service is causing problems.

In short:

• Use Safe Mode when Windows won’t start correctly, or you have major driver issues.
• Use a clean boot when Windows starts, but something keeps crashing or misbehaving, and you suspect installed software.

How to perform a clean boot in Windows 11 and 10

A clean boot lets you troubleshoot conflicts between apps and drivers, and here’s how to do it on Windows 11.

Note: The process for a clean boot on Windows 11 and Windows 10 is the same.

• Press Windows + R, type msconfig, and ok to open the Windows configuration window.
• Under the General tab, select the option Selective startup
• Then uncheck the “Load startup items” checkbox.
• Make sure the Load system services and Use original boot configuration is checked

• Next, go to the Services tab, check the box Hide all Microsoft services at the bottom. (You will find it at the bottom of that window.)
• This is very important. It hides essential Windows services so you don’t accidentally disable them.
• Now, click on Disable all. This disables all non‑Microsoft services (third‑party services installed by your software).

• Now go to the Startup tab and click Open Task Manager. The Task Manager window will open on the Startup tab.

For each startup item that is enabled and comes from third‑party software, right‑click it and choose Disable.

• Leave essential items from Microsoft or your device manufacturer if you know they are required.
• If you are not sure, you can disable most items; you can always re‑enable them later.

• Close Task Manager.
• Back in the System Configuration window, click OK.
• You will be prompted to restart your computer. Click Restart.

After the restart, your PC will be in a clean boot state – only essential Microsoft services and drivers plus a minimal set of programs will be running.

How to Use Clean Boot to Find Problematic Apps and Services

Now that Windows is in a clean boot state, you can test whether the original problem persists.

1. Check if the issue still happens in clean boot

• If the problem is gone in clean boot, it strongly suggests that a third‑party service or startup program was causing it.
• If the problem still occurs, the issue may be with a Windows component, driver, or hardware rather than third‑party software.

2. Re‑enable services and startup programs in groups

To find the exact cause:

1. Open msconfig again (Windows key + R → msconfig).
2. On the Services tab, check Hide all Microsoft services.
3. Re‑enable about half of the disabled services by checking them.
4. Click Apply and restart.

• If the issue returns → The problem is in that group you just re‑enabled.
• If the issue does not return → The problem is in the other group (still disabled).

Repeat this process, narrowing down:

• Keep splitting the group of enabled services until you find the single service that causes the issue.

Do a similar process with startup items in Task Manager:

1. Open Task Manager (Ctrl + Shift + Esc) and go to the Startup tab.
2. Re‑enable startup items in small groups.
3. Restart and test after each change.

Once you identify the specific service or startup program that causes the problem, you can:

• Leave it disabled, or
• Uninstall or update the problem application, or
• Contact the software vendor for support.

How to Return Windows to Normal Startup After a Clean Boot

To return to normal boot, Just need to undo the changes you have done and restart your PC.

• Press Windows key + R, type msconfig, and press Enter.
• On the General tab, select Normal startup.
• Go to the Services tab and uncheck the box Hide all Microsoft services to see everything.
• Ensure the services you want are checked. If you are not sure, you can click Enable all, then later disable any third‑party services you don’t need.
• Go to the Startup tab and click Open Task Manager.
• In Task Manager → Startup tab, re‑enable the startup items you want by right‑clicking and selecting Enable.
• Close Task Manager and click OK in the System Configuration window.
• Restart your computer.

Windows should now start in normal mode, with all chosen services and startup items running.

Is a Clean Boot Safe? What It Does and Does Not Do

A clean boot is generally safe and is recommended by Microsoft for troubleshooting software conflicts.

A clean boot DOES:

• Temporarily disable non‑Microsoft services.
• Temporarily disable third‑party startup programs.
• Help you identify whether a background program is causing issues.

A clean boot DOES NOT:

• Delete your personal files (documents, photos, etc.).
• Uninstall any of your programs.
• Reset Windows or remove user accounts.
• Fix hardware problems such as bad RAM or failing disks.

If your problems persist even in a clean boot state, the issue may be related to:

• Hardware (RAM, disk, CPU, etc.).
• A corrupted Windows component (use SFC/DISM).
• A driver loaded even in clean boot.

In those cases, you should also consider:

• Running Windows Memory Diagnostic to check RAM.
• Running CHKDSK to check disk for errors.
• Running SFC and DISM to repair system files and the Windows image.

Frequently Asked Questions About Clean Boot

Does a clean boot delete my files or programs?

No. A clean boot does not delete your personal files or uninstall programs. It only temporarily disables non‑Microsoft services and startup apps so you can troubleshoot software conflicts.

Is clean boot the same as Safe Mode?

No. Safe Mode loads Windows with a very limited set of drivers and a basic interface. Clean boot loads Windows normally but disables third‑party services and startup programs. Clean boot is mainly for finding problematic software that starts with Windows, while Safe Mode is used when Windows cannot boot normally or when core drivers are causing issues.

How often should I use clean boot?

You should use clean boot only when troubleshooting problems like crashes, freezes, or high resource usage that you suspect are caused by installed software. It’s not meant to be a permanent way of running Windows.

Can I leave my PC in clean boot mode permanently?

Technically, you can, but it is not recommended. Some apps, services or drivers you rely on may not run. A clean boot is a temporary diagnostic state. After you identify the problematic software and fix or remove it, you should return to normal startup.

What should I do if my problem persists even after a clean boot?

If the same problem occurs in a clean boot state, the cause is likely: A hardware issue (RAM, disk, overheating, etc.), or A core Windows component or driver that still loads even in a clean boot. Try running Windows built-in diagnostics like System File Checker, DISM, or System Restore, checking hardware (drivers, peripherals, memory)