Fixing Windows Boot Order Issue in Dual Booting Pop OS and Windows

Abstract: Resolve Windows overriding Pop OS in dual boot by manually setting GRUB as the primary boot device in UEFI firmware settings.

Created: 2026-10-03 by
To resolve the boot order issue where Windows overrides Pop OS in a dual-boot setup, you must manually adjust the boot priority within your system's UEFI firmware settings. This typically involves accessing the BIOS or UEFI menu by pressing a specific key during startup, locating the Boot Option Priorities section, and moving the GRUB bootloader to the first position. If the option is not visible, you may need to enable legacy support or check secure boot configurations.

Understanding the Boot Priority Conflict

When you install Windows after Linux, or when Windows updates its bootloader, it often registers itself as the primary boot device. The Unified Extensible Firmware Interface (UEFI) stores a list of preferred boot devices, and Windows tends to place its own boot manager at the top of this list. Consequently, when you power on your ASUS machine, it immediately launches Windows, bypassing the GRUB menu that allows you to select Pop OS. This behavior is standard for Windows but problematic for users who wish to start with their Linux distribution by default.

The core of the problem lies in how the firmware interprets the boot entries. Unlike Legacy BIOS which relied heavily on the Master Boot Record (MBR), modern UEFI systems use NVRAM variables to store boot preferences. Windows modifies these variables aggressively to ensure fast startup times and compatibility features like Fast Boot. Therefore, simply reinstalling GRUB often does not fix the persistent boot order issue because the firmware setting remains unchanged until you intervene directly.

Accessing the BIOS/UEFI Settings

To change the boot order, you need to enter the firmware interface before the operating system loads. Since you are using an ASUS motherboard or laptop, the process is generally consistent across most models. Restart your computer and watch for the ASUS logo or the initial splash screen. You must press the designated key repeatedly as soon as the screen lights up. For most ASUS devices, this key is F2 or Delete. Some newer models may require you to press F8 to access the Boot Menu directly, but entering the full BIOS setup via F2 gives you more granular control over the boot priorities.

If you are running Windows 10 or 11 with Fast Startup enabled, the computer might boot too quickly to catch the key press. In this scenario, you can access the advanced startup options from within Windows. Navigate to Settings > Update & Security (or System in Win 11) > Recovery. Under Advanced startup, click Restart now. Once the system reboots into a blue menu, select Troubleshoot > Advanced options > UEFI Firmware Settings and click Restart. This will take you directly into the BIOS without needing to time the key press.

Adjusting the Boot Order in UEFI

Once inside the BIOS, the interface varies depending on whether you are in "Easy Mode" or "Advanced Mode." ASUS motherboards often default to a simplified view. Look for a button or link labeled Advanced Mode (often F7) to see the full range of options. Navigate to the Boot tab using the arrow keys or mouse. Here you will find a section titled Boot Option Priorities.

You should see a list of available boot devices. Look for an entry named ubuntu, pop-os, or GRUB. It might be listed under Boot Option #1, #2, etc. If Windows Boot Manager is currently at the top, you need to move the Linux entry above it. Select the Linux boot entry and use the keys indicated on the screen (usually +/- or F10/F11) to move it to the first position. Save your changes and exit, typically by pressing F10 and confirming Yes.

If you do not see a distinct GRUB or ubuntu entry, it is possible that the bootloader was installed in the EFI System Partition (ESP) but not registered correctly in the NVRAM. In this case, refer to our guide on BIOS won't recognize bootloader: Troubleshooting Guide to ensure the ESP is properly mounted and the bootloader files are intact.

Handling Secure Boot and Legacy Support

Some ASUS systems have strict security policies that interfere with custom boot loaders. Check the Security or Boot tab for Secure Boot. While Pop OS supports Secure Boot, misconfigurations here can sometimes cause the firmware to ignore third-party boot entries or prioritize signed Windows entries exclusively. If moving the boot order did not work, try temporarily disabling Secure Boot to see if the GRUB entry becomes selectable. You can re-enable it later if needed.

Additionally, ensure that CSM (Compatibility Support Module) is disabled if you installed Pop OS in UEFI mode. Mixing CSM and pure UEFI modes can lead to confusing boot lists. Your previous article on Dual Booting Pop OS and Windows likely covered the initial installation steps; verify that both OSes were installed in the same mode (preferably UEFI only) to avoid partition conflicts.

Verifying the Fix

After saving and exiting the BIOS, allow the computer to restart normally. You should now see the GRUB menu appear, giving you the choice between Pop OS and Windows. If Windows still boots automatically, repeat the BIOS steps and double-check that no other boot entries, such as network boot or USB drives, are interfering. You can also use the efibootmgr command in Pop OS to inspect and modify boot order from within Linux, providing a software-level backup to the hardware settings.

Frequently Asked Questions

Why does Windows keep taking over the boot order after updates?

Windows updates often include bootloader patches that reset the UEFI boot variables to ensure system stability and fast startup. Microsoft designs Windows to be the dominant OS on many consumer PCs, so it actively manages the boot sequence. To counter this, you may need to re-adjust the BIOS settings after major Windows updates, or use Linux tools to lock the boot order.

Can I set the boot order from within Pop OS instead of BIOS?

Yes, you can use the efibootmgr utility in Pop OS to view and modify boot entries. Running sudo efibootmgr -v shows the current order, and you can use flags like -o to set a new order. However, some firmware implementations ignore software changes and revert to hardware defaults, so BIOS adjustment remains the most reliable method.

What if I don't see GRUB in the BIOS boot list?

If GRUB is missing, the EFI System Partition may not be properly recognized. Ensure that the partition type is FAT32 and has the ESP flag set. You can mount the ESP and check for the /boot/grub/grub.cfg file. If files are present but not listed, you may need to reinstall GRUB using a Live USB and chroot into your Pop OS installation.

Does disabling Secure Boot affect my Windows installation?

Disabling Secure Boot prevents Windows from verifying the integrity of the bootloader and kernel modules. While Windows 10 and 11 will still run, features like BitLocker drive encryption might require recovery keys to unlock upon reboot. Additionally, some gaming anti-cheat software requires Secure Boot to be enabled, so weigh the trade-offs before changing this setting.

How do I access the boot menu on an ASUS laptop?

On most ASUS laptops, pressing F8 repeatedly during startup opens the one-time Boot Menu. This allows you to select a boot device for that session only without changing the permanent BIOS settings. If F8 does not work, try Esc or enter the BIOS via F2 and navigate to the Boot tab to change the permanent priority.

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