Tools: How to Remove Orphan Linux Boot Entries from Windows 11 UEFI (2026)

Tools: How to Remove Orphan Linux Boot Entries from Windows 11 UEFI (2026)

Summary

Technical Background

EFI System Partition (ESP)

NVRAM Boot Entries

Step 1 — Mount EFI Partition

Step 2 — Remove Linux Bootloader Files

Permission Errors

Step 3 — Remove NVRAM Boot Entries

3.1 List firmware entries

3.2 Identify entries to remove

3.3 Delete orphan entry

Step 4 — Remove drive letter

Troubleshooting

Problem 1 — Access denied

Problem 2 — delete fails

Problem 3 — entry still appears

Problem 4 — Windows does not boot

Commands Used

Version Notes

Tested Environment

Disclaimer Level: Intermediate

Estimated Time: 15–20 minutesOperating System: Windows 11 (UEFI systems) After replacing a Linux installation (such as Pop!_OS, Ubuntu, or Arch Linux) with Windows 11, old boot entries may remain visible in UEFI firmware. This happens because UEFI boot configuration is stored in: Both must be cleaned. ⚠️ Before you start: Backup your data. Modifying the EFI partition or NVRAM entries can make your system unbootable if done incorrectly. The EFI System Partition (ESP) is a FAT32-formatted partition that stores the bootloaders for all installed operating systems. On Windows systems, it typically ranges from 100–500 MB in size and is labeled as "System". UEFI firmware stores boot entries in non-volatile memory. Removing EFI files does not remove NVRAM entries. Open Command Prompt as Administrator. ⚠️ Replace 0 with your system disk number. ⚠️ Replace 1 with the EFI partition (~100–500 MB, Type: System) Remove Linux folders: 💡 On Portuguese Windows, use /d s instead of /d y. Remove entries that reference: Method 1 — Startup Repair Method 2 — Recovery Command Prompt ✅ Quick Checklist (click to expand) Backup before modifying EFI partition.

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Code Block

Copy

EFI/ ├── Microsoft/ ├── Boot/ ├── pop_os/ ├── systemd/ ├── ubuntu/ └── linux/ EFI/ ├── Microsoft/ ├── Boot/ ├── pop_os/ ├── systemd/ ├── ubuntu/ └── linux/ EFI/ ├── Microsoft/ ├── Boot/ ├── pop_os/ ├── systemd/ ├── ubuntu/ └── linux/ list disk select disk 0 list partition list disk select disk 0 list partition list disk select disk 0 list partition select partition 1 assign letter=Z exit select partition 1 assign letter=Z exit select partition 1 assign letter=Z exit Z: cd \EFI dir Z: cd \EFI dir Z: cd \EFI dir rmdir /s /q systemd rmdir /s /q pop_os rmdir /s /q systemd rmdir /s /q pop_os rmdir /s /q systemd rmdir /s /q pop_os takeown /f systemd /r /d y takeown /f systemd /r /d y takeown /f systemd /r /d y icacls systemd /grant Administrators:F /t icacls systemd /grant Administrators:F /t icacls systemd /grant Administrators:F /t rmdir /s /q systemd rmdir /s /q systemd rmdir /s /q systemd bcdedit /enum firmware bcdedit /enum firmware bcdedit /enum firmware Firmware Application (101fffff) ------------------------------- identifier {29c75bf6-3303-11f1-b7f4-e7fe7d8485ec} device partition=\Device\HarddiskVolume1 path \EFI\systemd\systemd-bootx64.efi description Pop!_OS Firmware Application (101fffff) ------------------------------- identifier {bootmgr} device partition=\Device\HarddiskVolume2 path \EFI\Microsoft\Boot\bootmgfw.efi description Windows Boot Manager Firmware Application (101fffff) ------------------------------- identifier {29c75bf6-3303-11f1-b7f4-e7fe7d8485ec} device partition=\Device\HarddiskVolume1 path \EFI\systemd\systemd-bootx64.efi description Pop!_OS Firmware Application (101fffff) ------------------------------- identifier {bootmgr} device partition=\Device\HarddiskVolume2 path \EFI\Microsoft\Boot\bootmgfw.efi description Windows Boot Manager Firmware Application (101fffff) ------------------------------- identifier {29c75bf6-3303-11f1-b7f4-e7fe7d8485ec} device partition=\Device\HarddiskVolume1 path \EFI\systemd\systemd-bootx64.efi description Pop!_OS Firmware Application (101fffff) ------------------------------- identifier {bootmgr} device partition=\Device\HarddiskVolume2 path \EFI\Microsoft\Boot\bootmgfw.efi description Windows Boot Manager bcdedit /delete {29c75bf6-3303-11f1-b7f4-e7fe7d8485ec} /f bcdedit /delete {29c75bf6-3303-11f1-b7f4-e7fe7d8485ec} /f bcdedit /delete {29c75bf6-3303-11f1-b7f4-e7fe7d8485ec} /f diskpart select disk 0 select partition 1 remove letter=Z exit diskpart select disk 0 select partition 1 remove letter=Z exit diskpart select disk 0 select partition 1 remove letter=Z exit takeown /f systemd /r /d y icacls systemd /grant Administrators:F /t rmdir /s /q systemd takeown /f systemd /r /d y icacls systemd /grant Administrators:F /t rmdir /s /q systemd takeown /f systemd /r /d y icacls systemd /grant Administrators:F /t rmdir /s /q systemd bcdboot C:\Windows /s Z: /f UEFI bcdboot C:\Windows /s Z: /f UEFI bcdboot C:\Windows /s Z: /f UEFI - EFI System Partition (ESP) - UEFI NVRAM boot entries - GUID identifier - Description - Path to EFI loader - Device reference - /s → removes directories recursively - /q → quiet mode (no confirmation) - /f → target folder - /r → recursive - /d y → auto confirm - /f → force deletion without confirmation - entry already removed - firmware protected entry - invalid reference - remove EFI files first - firmware cache - fallback recreated - reboot twice - load BIOS defaults - update BIOS - Boot Windows installer USB - Repair your computer - Startup Repair - [ ] Backup completed - [ ] Disk/Partition numbers verified - [ ] Microsoft/ and Boot/ preserved - [ ] {bootmgr} and {current} not deleted - [ ] Drive letter removed - Windows 11 24H2 - UEFI firmware - Pop!_OS systemd-boot