Fixing Windows bootloader after installing Linux (dual-boot)

Windows does not like it when you install Linux after it


I had been running a dual-boot system for 2 years since my current PC was first built. I have one NVMe drive running Windows 11 and another NVMe drive running Fedora. This was a way for me to separate my Linux workstation from my Windows gaming drive. However, I would eventually do all development work on Windows anyway.

So, I decided to spice things up and try out Kubuntu, a super customizable flavor of Ubuntu, and do a fresh install. The installation went well, but something went wrong on reboot.


Upon rebooting, I noticed that my Windows boot had gone missing. The only bootable disk I had listed in BIOS was my newly installed Kubuntu. So, I tried changing the boot settings to see if there were other available boot options. I found a few leftover Windows boot partitions from my storage drives that I forgot to clear, but those weren't the drives I needed to boot to. I spent several hours during the weekend searching for a solution and finally found one.

Repair Windows EFI Partition After a Linux Installation


  • Prepare Windows 11 installation media on a USB drive and boot to it.

  • Start Windows 11 installation process, but click the following links to open a command prompt.

Repair your computer -> Troubleshoot -> Advanced -> Command Prompt

  • Run diskpart in the command prompt

Microsoft DiskPart version 10.0.22621.1
Copyright (C) Microsoft Corporation.

  • Run list vol to list the volumes and note the letter of the drive you want to boot into
DISKPART> list vol

Volume ###    Ltr  Label          Fs     Type        Size     Status     Info
------------  ---  -------------  -----  ----------  -------  ---------  --------
Volume 0       F   SSD Storage    NTFS   Partition    931 GB  Healthy
Volume 1       D   Old 1TB HDD    NTFS   Partition    931 GB  Healthy
Volume 2       E   New 2TB HDD    NTFS   Partition   1863 GB  Healthy
Volume 3       C   Game Drive     NTFS   Partition    931 GB  Healthy
Volume 4                          NTFS   Partition    701 MB  Healthy    System
  • If the volumes you want aren't assigned a letter, assign them like so
DISKPART> sel vol 3
DISKPART> assign letter=C
  • C drive is what I want, so I can exit diskpart now

  • Run bcdboot to copy the Windows boot files from C drive onto itself, in both UEFI and BIOS formats. You can also copy the boot files to another drive if you wish.
C:\Users\user> bcdboot c:\Windows /s c: /f ALL

After doing this, I was able to boot to my Windows drive from BIOS.


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