I've encountered a frustrating issue three times now. I've got Windows set up on `/dev/sda`, and then I install a Linux distro on `/dev/nvme0n1`. Each time, Windows EFI disappears completely. I'm puzzled because the Linux installation shouldn't have affected `/dev/sda` at all. I can even see the files in the 650 MB partition, which include folders like 'System Volume Information' and a recovery folder. What could be happening? I've tried using rEFInd, but it can't find any bootloaders because, as far as I can tell, they've just vanished. Even GRUB didn't help. It feels like Windows is somehow sabotaging itself. I need a way to install Linux without losing access to Windows. Also, just to clarify, this isn't about needing help with Windows support—I'm trying to understand what's going wrong here.
5 Answers
What distro are you using, and how are you installing it? Some automated installers like Mint may default to placing GRUB in the active EFI partition regardless of where the OS itself is installed. If you're working with dual drives, it might be best to disconnect the Windows drive during Linux installation, or at least adjust the partitioning manually. That way, you can avoid these cross-drive issues.
A lot of Linux distros will default to using an existing boot/EFI partition on other drives instead of creating their own. It's essential to set up a FAT32 boot/EFI partition on the drive where Linux is installed and make sure to set the right flags. If you don’t change those flags, you might run into problems like you did. So, yeah, check that out!
But in this case, Linux didn’t affect the other drives, as I checked and no modifications were made outside the installation drive. Windows, however, installed its EFI on the NVMe drive without my consent. That's what led to the problem.
If you didn't unplug the Windows disk before the Linux install, the installer might write GRUB files to the Windows EFI partition regardless of your selections during installation. There's a guide available that details the right approach for dual-booting with two separate disks, which might help you avoid future problems.
In my case, even if I had disconnected the Windows drive, it wouldn't have mattered. Windows placed its EFI on the NVMe, which I ended up wiping. Linux didn't affect the SSD at all—it was purely a Windows decision. Disconnecting drives shouldn't have to be the first course of action to prevent these issues.
I usually pull all drives except the target one when installing an OS. This method has worked wonders for me; I rarely have these kinds of problems. It seems odd that an installer would touch the bootloaders of inactive drives, but it happens more often than you'd think.
What I discovered was that Windows moved its EFI to the NVMe drive despite me telling it to install on the SSD. This pattern is unsettling—it feels like Windows doesn't respect our system choices. I manually fixed the location of the EFI, and now everything boots just fine.
I had the same issue with Fedora 42 recently! My Windows installation became unbootable after installing Linux. It's such a pain trying to figure out how to do it right.
If your goal is to install Windows again, I recommend downloading the ISO and setting it up on Ventoy—it’s pretty straightforward.
I've dealt with this a few times now using various distros. I find it frustrating to disconnect drives. Each Linux install has been managed carefully, with only the selected partition being modified so I’m still not sure why the EFI issue persists.