Windows Run CHKDSK on Every Boot? – How To Fix It

Why Does CHKDSK Run Every Startup & How To Fix It? |

CHKDSK in Windows performs the vital function of identifying the bad sector on your disk drives. 

Windows has many built-in systems to trace and remove bad sectors and malware. These systems are an essential part of your operating system. This might be a bug if your Windows runs the CHKDSK simultaneously after each restart.

If you are facing the same issue, then here’s the thorough guide you are looking for. Let’s start directly with the solutions.

Why Does CHKDSK Run Every Boot/Startup?

Sometimes Windows keeps finding problems that require multiple scans to fix. To ensure that all errors are detected and removed, it performs the CHKDSK scan repeatedly. Moreover, a stuck file error or corruption may lead to recurring CHKDSK scans.

CHKDSK, or check disk, is a Windows feature that runs to recover and repair broken files after problems like sudden system shutdowns, disk errors, registry damage, excessive drive fragmentation, and malware. Moreover, it also performs analysis and is able to detect bad sectors in your storage device. 

First of all, always allow the CHKDSK to complete the scan. If you won’t allow the scan to complete, it may not remove the error and will run every startup. Moreover, canceling the CHKDSK scan may lead to improper Windows functioning and bugs, as the corrupted field has not been repaired. 

Improper System Shutdown

If your computer shuts down unexpectedly or improperly, a CHKDSK scan can be initiated at the next startup. It happens because Windows wants to ensure the system files are not affected after an abnormal shutdown.

CHKDSK also repairs broken or corrupted files, if there are any. It assists in recovering the previous version of Windows, which may have become corrupted as a result of an unexpected shutdown.

  • How To Solve It? 

Try to shut down your computer properly by closing all the applications and saving all your data. Always look for background processes. If any application runs in the background, close it properly before turning off your PC. Moreover, ensure your PC is completely shut down before plugging out the power cable from the power source. 

Why Does CHKDSK Run Every Startup & How To Fix It? |

Disk Errors 

Errors or inconsistencies in your hard disk drive, such as bad sectors, corrupt files, or file system errors, can cause CHKDSK to run every startup. Windows detect these errors as serious issue, and it starts to resolve them by checking the disks and repairing the files. 

  • How To Fix It?

Open the command prompt as an administrator. Type “chkdsk C: /f /r” (replace the “C:” with the drive letter where you have an error). Press Enter to confirm the scheduled scan on the next restart. Restart the computer and use CHKDSK to complete the scan and correct the disk error.

Why Does CHKDSK Run Every Startup & How To Fix It? |

Registry Damage

Sometimes incorrect registry settings can cause CHKDSK to execute repeatedly. It can happen if any registry entries associated with CHKDSK have been changed or corrupted. It can also occur if the registry files of your operating system are corrupted and have bugs in them. 

  • How To Fix It?

You can disable the CHKDSK registry file from the registry menu. To do that, press “Windows + R” and open RUN. Now type “Regedit.exe” and hit enter. Now navigate to “HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Session Manager.” Here, double-click on “BootExecute.” Now change “autocheck autochk * /” to “autocheck autochk *” and click OK to confirm.

Why Does CHKDSK Run Every Startup & How To Fix It? |

You can restore previous registry file backups using the registry editor. Open the registry edit windows and click “File” to open the file menu. Select “Import” and select the previous registry backup from the next Windows. Finally, it will restore the previous registry files and remove the registry damage.

Why Does CHKDSK Run Every Startup & How To Fix It? |

File System Corruption 

If the file system on your hard drive is corrupted, Windows automatically schedules CHKDSK to run at startup to detect and correct any errors. Corruption can occur due to software bugs, malware infections, or accidental system outages.

  • How To Fix It?

The best technique to tackle this situation is to run an SFC scan. This scan analyzes the corrupted files and repairs them automatically. To do SFC scan, open the command prompt as an administrator. Type the command “sfc /scannow.” Press Enter to allow System File Checker to locate and repair any corrupted system files. Restart the computer and verify that the CHKDSK scan runs at every startup.

Why Does CHKDSK Run Every Startup & How To Fix It? |

Drive Fragmentation

Over time, files on your hard drive can become fragmented, which means they are scattered in different places. CHKDSK can be enabled during startup to aggregate fragmented files and improve system performance. These file fragmentations may have corrupted files scattered with the disk, leading to recurring CHKDSK at startup.

  • How To Fix It?

In Windows, you can access the Disk Defragmenter tool by typing “defrag” in the search bar and selecting the “Defragment and Optimize Drives” option from the results. Select the drive you want to partition and click the “Analyze” or “Optimize” button. 

Once the check is done, you will see a report showing how your disk is fragmented. It will determine whether separation is recommended or not. If the number of divisions is high, it is better to proceed with division.

Why Does CHKDSK Run Every Startup & How To Fix It? |

Malware Infections

Certain types of malware, such as viruses or rootkits, can effectively interfere with the operation of your file system. To detect and fix malware-related damage, Windows can initially run CHKDSK.

  • How To Fix It?

Make sure your antivirus software is up to date with the latest version. It will help identify and eliminate any bad malware and viruses detected. Start a thorough scan of your entire system with your updated antivirus software. Allow the scan to be completed and follow up on any indications to remove or contain the detected malware. Moreover, you can also run a Windows scan to detect potential viruses and malware.

How To Cancel Scheduled CHKDSK Scan?

You can cancel the scheduled CHKDSK using the command prompt. CHKDSK is typically programmed to run at specific intervals to actively monitor the health of the file system and the hard disk. It helps prevent data corruption, detects early signs of hardware failure, and ensures overall system stability.

To cancel the scheduled check disk scan, press Windows key + R, type “cmd,” and press enters to open the command prompt. Type “chkntfs /x C:” in the command prompt window and press enter. Replace “C:” with the drive letter running CHKDSK.

This command cancels a scheduled CHKDSK scan on the specified drive. Restart the computer and verify that CHKDSK is still running at startup.

Why Does CHKDSK Run Every Startup & How To Fix It? |

Is It Safe To Stop or Skip CHKDSK?

Interrupting or stopping CHKDSK scanning a disk may leave underlying file system problems unresolved. It can cause file corruption, data loss, and more disk problems down the line. Moreover, over time, the disk creates fragments to store data. Fragments hinder performance CHKDSK fixes this.

Suppose you encounter a difficult situation where your computer is frozen or you cannot take the time to complete the CHKDSK. In that case, you have no choice but to force a shutdown, but this should be a last resort and only be done when necessary.

CHKDSK is an important tool for managing the health and integrity of your computer’s file system and disk. While it is generally not recommended to stop or skip CHKDSK, there may be situations where it is necessary or relatively safe. 

However, it is important to understand the potential risks and perform regular disc inspections to minimize any issues. Moreover, by prioritizing the health of your disk and addressing discovered issues quickly, you can ensure the reliability and longevity of your system.

Why Does CHKDSK Run Every Startup & How To Fix It? |


CHKDSK is a Windows product that finds and repairs corrupt files, detects disk errors, and scans for bad areas. Several factors can cause CHKDSK to fail repeatedly during startup, including improper system shutdown, disk errors, registry corruption, file system corruption, drive fragmentation, and malware infection.

To solve the problem, it is important to allow CHKDSK to complete its scan when it is initialized to avoid premature termination. Moreover, Turning off the computer properly, ensuring that no external systems are connected, and avoiding sudden power outages can help prevent CHKDSK from unnecessarily functioning due to inappropriate system shutdowns.

Additionally, registry corruption can also cause repeated executions of CHKDSK. Changing the registry settings associated with CHKDSK or restoring a previous registry backup using the registry editor can help fix this problem.

Moreover, malware infections can interrupt the file system and trigger a CHKDSK scan. Ensuring antivirus software is up to date and performing a full system scan can help detect and remove malware.

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