[Boot Repair] How to Fix Windows Won’t Boot After CHKDSK

Why Windows won’t boot after CHKDSK?

CHKDSK (short for “Check Disk”) is a built-in tool in Windows that checks your hard drive for problems. It can fix file system errors, find bad sectors, and try to recover data from damaged parts of the drive. Normally, it helps improve your system's health. But sometimes, after running CHKDSK, Windows may not start properly.

When CHKDSK runs, it checks and repairs the file system. But if something goes wrong—like a shutdown during the scan or deeper hard drive problems—it may cause key system files to go missing or get damaged. This can stop Windows from loading normally.

Common signs include:

♦️PC stuck in boot loop, and the computer keeps restarting.

♦️A missing boot device message, meaning your system can't find the drive with Windows on it.

♦️A black screen that appears after the logo and never moves on.

Now that you know why this problem happens, let’s look at the solutions to get your system working again.

How to fix pc won't boot after disk check?

If the system won't boot after CHKDSK, you can follow the 4 fixes. The first method can also help to fix many other boot issues like BSOD, PC stuck in boot loop, and so on.

Fix 1. Perform a boot repair

Incorrect use of CHKDSK can damage the Master Boot Record (MBR) or delete Boot Configuration Data (BCD) files. These are essential for starting Windows. If they’re corrupted or missing, your system may fail to boot or freeze at the login screen.

AOMEI Partition Assistant offers a simple, risk-free way to repair these issues. Its Boot Repair feature fixes BCD errors and other startup problems with just a few clicks—no technical skills needed.

AOMEI Partition Assistant

The Best Windows Disk Partition Manager and PC Optimizer

Free Download
Windows 11/10/8.1/8/7

Step 1. Install and launch AOMEI Partition Assistant on a working PC, click "Recover"-"Boot Repair" and then click the "create a bootable disk" option to create a WinPE "Boot Repair" disk.

Step 2. Boot the PC that cannot boot into WinPE. It will automatically load the Boot Repair tool and start the boot entries scan process. All boot entries will be displayed.

Advanced Settings (Select a location to store the repaired boot entry):

Repair to the current disk: The system will boot from the current disk and ensure the boot files are complete and functioning properly. (By default)

Repair to another disk: This operation will repair the boot entry or create a new system boot entry to ensure the system can boot from the disk you select.

You can either repair to the current disk or repair to another disk. Repair to the current disk is recommended for common users.

Step 3. Select one/multiple repairable boot entries you want to repair and click the "Repair" button to start the boot repair.

Step 4. Wait for the repair process to finish. Once it is finished, you can check the repair result. If it succeeds, you will get a "Repair Successfully" result.

Fix 2. Remove all peripherals

Sometimes, external devices may disrupt the boot process. To check for this issue:

Step 1. Unplug all unnecessary devices like USB drives or external hard disks.

Step 2. Restart your computer and see if it starts up correctly.

Fix 3. Run System Restore

Step 1. Restart your PC a few times during the boot until the Automatic Repair message appears.

Now go to Troubleshoot > Advanced options > System Restore.

Step 2. Select your username and enter your password. Click on Next, select the desired restore point and follow the instructions on the screen to restore your PC.

After your PC is restored, check if the problem still appears.

Fix 4. Reinstall your Windows PC

If nothing else works and Windows still won’t start after CHKDSK, reinstalling Windows might be your only option. This will remove all your files and settings, so only use this method as a last resort. Before you begin, please back up any important data to avoid losing it. You’ll need a Windows installation USB or DVD to proceed.

Step 1. Restart your PC a few times until you start Automatic Repair.

Step 2. Choose Troubleshoot > Reset this PC > Remove everything.

Step 3. For the next step you might be asked to insert Windows installation media, so be sure to have it ready.

Step 4. Now select your version of Windows and click on Only the drive where Windows is installed > Just remove my files. You should now see a list of changes that reset will perform. If you’re ready to start, click on the Reset button. Then you need to follow the rest directions to complete the job.

When the reset is finished, you will have a fresh installation of Windows and the problem should be resolved permanently.

Conclusion

CHKDSK is a useful tool for fixing disk errors, but if problems occur during or after the scan, Windows won’t boot after CHKDSK. Issues like damaged boot files, corrupted system data, or bad sectors can all lead to startup failure. Fortunately, there are several ways to fix this, such as performing boot repair with a handy tool, AOMEI Partition Assistant, removing external devices, using System Restore, or reinstalling Windows. By following these steps, you can restore your system.

AOMEI Partition Assistant

The Best Windows Disk Partition Manager and PC Optimizer

Free Download
Windows 11/10/8.1/8/7