Windows Won't Boot After Running CHKDSK: How to Fix?

Updated by

Roxanne 

Written by

Cici 

Updated on Apr 28, 2025

CHKDSK, short for Check Disk, is a built-in Windows utility designed to scan and repair hard drive file system errors and bad sectors. While it is generally a helpful tool, there are instances where it can lead to boot problems. EaseUS will explore the reasons behind this issue and provide step-by-step solutions to help you regain access to your system.

Why Windows Won't Boot After CHKDSK?

We collected some potential causes of this boot problem:

• Corrupted File System: If CHKDSK encounters errors that cannot be fixed, it may leave the file system in an inconsistent state.
• Bad Sectors: Physical damage to the hard drive can lead to data loss during the CHKDSK process.
• Interruption During CHKDSK: Turning off the computer while CHKDSK is running can cause corruption.
• Compatibility Issues: Running an older version of CHKDSK on a newer file system (like NTFS) can lead to unexpected results.

When CHKDSK runs, it checks the integrity of the file system and attempts to fix any detected errors. However, if the process is interrupted or there are underlying issues with the hard drive, it can result in a corrupted file system or even missing boot files. Common symptoms include:

• Boot Loop: The computer repeatedly attempts to boot but fails.
• Black Screen: The system may hang on a black screen after the manufacturer logo.
• Missing Boot Device: BIOS may not recognize the hard drive where Windows is installed.

Now we have learned the overview of this boot failure after running CHKDSK, let's dive into the solid ways to fix this issue:

How to Fix Windows Won't Boot After Running CHKDSK - 6 Ways

1. Way 1. Remove Unnecessary Peripherals
2. Way 2. Run Boot Repair Tool
3. Way 3. Apply Windows Startup Repair
4. Way 4. Rebuild BCD and MBR via Command Prompt
5. Way 5. Use CHKDSK in WinRE
6. Way 6. Perform a System Restore
7. Way 7. Reinstall the Windows System

Way 1. Remove Unnecessary Peripherals

Sometimes, external devices can interfere with the boot process. To troubleshoot:

• Disconnect all non-essential peripherals (e.g., USB drives and external hard drives).
• Restart your computer to see if it boots normally.

Way 2. Run Boot Repair Tool

When facing the issue of Windows not booting after running CHKDSK, EaseUS Partition Master Professional emerges as a comprehensive solution. This powerful software provides various tools designed to address partition-related problems and recover from system failures effectively.

Step 1. Start EaseUS Partition Master after connecting the external drive/USB to your computer, go to "Bootable Media," and click "Create bootable media."

Step 2. Select an available USB Drive or CD/DVD and click "Create." You can also burn the Windows ISO file to the storage media.

Step 3. Connect the created bootable drive to the new computer and reboot the computer by pressing and holding F2/Del to enter the BIOS. Then, set the WinPE bootable drive as the boot disk and press F10 to exit.

Step 4. Boot the computer again and enter the WinPE interface. Then, open EaseUS Partition Master and click "Boot Repair" under the "Toolkit" option.

Step 5: Select the system you want to repair and click "Repair."

Step 6. Wait a moment, and you will receive an alert that the system has been successfully repaired. Click "OK" to complete the boot repair process.

Way 3. Apply Windows Startup Repair

If removing peripherals and boot repair doesn't resolve the issue, you can try accessing WinRE to run Startup Repair, which can automatically fix certain problems that prevent Windows from starting::

• Force Shutdown: Hold the power button until your computer shuts down completely.
• Restart and Repeat: Turn it back on and repeat this process three times until you see "Preparing Automatic Repair."
• Select Advanced Options: Once in WinRE, navigate to Troubleshoot > Advanced options.
• In WinRE, select Startup Repair.
• Follow the prompts and let Windows attempt to fix any detected issues.

Now, let's share this post with more users:

Way 4. Use CHKDSK in WinRE

If you choose Command Prompt, you can run the following commands to try and fix the "Windows won't boot after CHKDSK" problem:

Step 1. Type "chkdsk /f /r C:" (replace "C:" with the drive letter of your Windows installation) and press Enter to run CHKDSK with the repair and recovery options.

Step 2. Type "bootrec /rebuildbcd" and press Enter to rebuild the Boot Configuration Data.

Step 3. Type "bootrec /fixmbr" and press Enter to fix the Master Boot Record.

Step 4. Type "bootrec /fixboot" and press Enter to fix the boot sector.

Way 5. Perform a System Restore

If Windows won't boot after CHKDSK, you can try using System Restore to revert your system to a previous state when it was working correctly. System Restore is a Windows feature that allows you to undo changes to your system settings and files, effectively restoring your computer to a previous point in time.

To use System Restore, follow these steps:

Step 1. Boot into Safe Mode as described in the previous step.

Step 2. Press the Windows key + R to open the Run dialog box.

Step 3. Type "rstrui.exe" in the Run dialog box and press Enter.

Step 4. The System Restore wizard will open. Follow the on-screen instructions to choose a restore point and restore your system.

After completing the System Restore process, restart your computer and check if Windows boots up successfully. If System Restore doesn't fix the issue, move on to the next step.

Way 6. Reinstall the Windows System

If all else fails and Windows still won't boot after CHKDSK, you may need to consider reinstalling Windows to resolve the issue. Reinstalling Windows will erase all your files and settings, so it should be considered a last resort.

Before reinstalling Windows, make sure to back up any important files and data to avoid losing them. You can reinstall Windows using a Windows installation disc or USB drive. Follow the on-screen instructions to reinstall Windows and set up your system from scratch.

• Back up any important data if possible.
• Use a Windows installation media (USB or DVD) to boot into the setup.
• Choose Install Now, then select Custom Installation for formatting options.

After reinstalling Windows, check if the "Windows won't boot after CHKDSK" problem has been resolved. If the issue persists even after reinstalling Windows, there may be a hardware problem with your computer that requires professional assistance.

Conclusions

Dealing with a non-booting Windows system after running CHKDSK can be daunting but is often resolvable through systematic troubleshooting. By following these steps—removing peripherals, accessing recovery options, and using repair tools like Startup Repair and Command Prompt commands—you can potentially restore your system without extensive technical knowledge. However, always prioritize data safety by backing up important files before proceeding with repairs or reinstallation efforts.

For tech-novice, we recommend EaseUS Partition Master to perform a reliable and effective boot repair.

FAQs on How to Fix Windows Won't Boot After CHKDSK

If you have further queries about Windows startup issues after running CHKDSK, you can refer to this FAQ part and find answers:

1. Why does running CHKDSK cause a Windows boot error?

CHKDSK is designed to scan and repair file system errors on hard drives. However, there are several reasons why running this utility may result in boot errors:

• Corruption of System Files
• Bad Sectors on Hard Drive
• Interruption During Process
• Incompatibility with Certain Drives

2. What are the disadvantages of CHKDSK?

While CHKDSK is a valuable tool for maintaining disk health, it has several disadvantages:

• File Fragmentation: Running CHKDSK can sometimes lead to file fragmentation.
• Risk of Data Loss: Running CHKDSK can lead to permanent data loss
• Limited Recovery Capabilities: While CHKDSK can fix file system errors, it is not a data recovery tool.

3. What can CHKDSK do?

CHKDSK is a Windows utility that scans disks for errors, attempts to repair file system issues, and identifies bad sectors, thereby helping maintain the overall health of the storage device.