why does bootloader always get messed up when dual boot installing on another drive?

link626 · Sunday at 11:19 PM

i have windows 11 installed on nvme1, including the efi partition.

the other drives don't have an efi partition.

after removing nvme1, i go and install another version of windows for testing purposes on ssd2 with 90gb unallocated space.
Installation creates the new efi partition, etc on ssd2.

With ssd2 still in the pc, when i put nvme1 back into the pc, it's own efi partition and all, and go to the bios to boot from nvme1, Windows boots into the repair screen.
It fails to boot into windows.

NVME1 and SSD2 each have their own efi partition. So why wasn't windows able to boot into NVME1 ?

NVME1 was removed and untouched during the installation of windows on SSD2.

I had to run the bcdboot command to fix nvme1.

XxXxX · Monday at 1:46 AM

because each time you install Windows that version of Windows tries to take over the boot sequence
the Windows boot-loader doesn't like living with anything else other then the last boot-loader version you installed.

this maybe of interest if you are dual booting with different versions of Windows
Grub2Win

Grub2Win

Download Grub2Win for free. ** Support has been added for Endeavour, MX Linux, Pop! OS, Zorin, and CachyOS.

sourceforge.net

its the Linux GRUB boot-loader for Windows.
best of luck Steve ..

link626 · Monday at 5:30 AM

XxXxX said:
because each time you install Windows that version of Windows tries to take over the boot sequence
the Windows boot-loader doesn't like living with anything else other then the last boot-loader version you installed.

this maybe of interest if you are dual booting with different versions of Windows
Grub2Win

Grub2Win

Download Grub2Win for free. ** Support has been added for Endeavour, MX Linux, Pop! OS, Zorin, and CachyOS.

sourceforge.net

its the Linux GRUB boot-loader for Windows.
best of luck Steve ..

so you're saying I should have deleted the efi partition of the newer windows on ssd2 before trying to boot into nvme1?

if efi on ssd2 is deleted, then it can see my original bootloader in nvme1?

i originally removed the nvme1 drive because when i installed windows on ssd2, it errored in the end due to having too many drives connected.

spapakons · Monday at 6:00 AM

I would leave NVME1 connected and then boot with the USB to reinstall Windows on the second disk. I would delete all partitions on second disk until all space is unallocated. Then proceed to install Windows on second disk. This should not affect NVME1 but add a second boot entry to boot into the second Windows installation. Only drawback it will make the second installation default and you would have to mark the first one default again.

PS: if the first disk doesn't boot, use the Repair Windows option in the USB.

link626 · Monday at 4:12 PM

spapakons said:
I would leave NVME1 connected and then boot with the USB to reinstall Windows on the second disk. I would delete all partitions on second disk until all space is unallocated. Then proceed to install Windows on second disk. This should not affect NVME1 but add a second boot entry to boot into the second Windows installation. Only drawback it will make the second installation default and you would have to mark the first one default again.

PS: if the first disk doesn't boot, use the Repair Windows option in the USB.

i originally left nvme1 connected when installing windows on ssd2.
but the install failed.

On ssd2 i have a data/storage partition in the back half I don't wanna delete.

i had a total of 5 hard drives connected, and i read that causes windows install to fail.
i guess i'm supposed to disconnect the other 3 drives.

windows was in the process of copying files to ssd2, and then threw an error in the end.

hsehestedt · Monday at 4:24 PM

spapakons said:
I would leave NVME1 connected and then boot with the USB to reinstall Windows on the second disk. I would delete all partitions on second disk until all space is unallocated. Then proceed to install Windows on second disk. This should not affect NVME1 but add a second boot entry to boot into the second Windows installation. Only drawback it will make the second installation default and you would have to mark the first one default again.

PS: if the first disk doesn't boot, use the Repair Windows option in the USB.

100% agreed. By leaving the other drive in, setup will see that there is already an EFI partition present and so it will not need to create another. It will also be able to update the boot config on that drive without creating that on the other drive.

The advice to remove other drives when doing a clean install is just fine for a single installation of Windows, not for dual booting.

spapakons · Monday at 5:50 PM

Especially when upgrading an unsupported computer, the upgrade might fail if you have two or more disks. Last time I upgraded my father's unsupported computer from 23H2 to 25H2 I disabled the second hard disk in Device Manager. The upgrade completed successfully. The first attempt, to upgrade from 23H2 to 24H2 failed because I hadn't done that.

Celery · Monday at 6:10 PM

Did I understand correctly that you currently have Windows 11 installed on NVMe1 and SSD2, but only the installation on NVMe1 boots?

If so, there is no need to delete the EFI partition on SSD2. Windows can have separate EFI partitions on different drives.

If your goal is to add the Windows installation on SSD2 to the boot menu used by NVMe1, run bcdboot against the Windows partition on SSD2 from the Windows installation on NVMe1. For example:

bcdboot D:\Windows

replacing D: with the correct drive letter for the Windows partition on SSD2.

Since you already restored the boot files on NVMe1 with bcdboot, the remaining step is simply to add the second Windows installation to the boot menu if that is your goal.

When setting up a PC to boot more than one operating system, you may sometimes lose the ability to boot into one of the operating systems. The BCDBoot option allows you to quickly add boot options for a Windows-based operating system.

BCDBoot Command-Line Options

learn.microsoft.com

Megahertz · Tuesday at 9:30 AM

There are two ways to have two drives, each one with an Win OS.
- You install Win on the first drive, then install Win on the second drive without disconnecting the first drive. During installation on the second drive, Windows installation wizard see that the first drive has a EFI partition and use it instead of creating a new EFI partition on the second drive. It install the second Windows boot manager on the EFI partition of the first drive. During boot it will always ask what drive you want to boot from. If you don't choose one it will select the first option.
The second drive isn't independent from the first as it doesn't have the EFI partition with the boot manager.

- You install Win on the first drive, disconnect the drive and then install Win on the second drive. Reconnect the first drive, set the priority boot drive on BIOS and when you want to boot the other drive you use the one time boot menu (F?) during POST. This way the two OS are independent, each OS is complete on its drive. This is the way I always do.

Megahertz · Tuesday at 9:35 AM

link626 said:
i have windows 11 installed on nvme1, including the efi partition.

the other drives don't have an efi partition.

after removing nvme1, i go and install another version of windows for testing purposes on ssd2 with 90gb unallocated space.
Installation creates the new efi partition, etc on ssd2.

With ssd2 still in the pc, when i put nvme1 back into the pc, it's own efi partition and all, and go to the bios to boot from nvme1, Windows boots into the repair screen.
It fails to boot into windows.

NVME1 and SSD2 each have their own efi partition. So why wasn't windows able to boot into NVME1 ?

NVME1 was removed and untouched during the installation of windows on SSD2.

I had to run the bcdboot command to fix nvme1.

You did what I described on the previous post. It should have worked

spapakons · Tuesday at 9:40 AM

If installing Windows on the second drive affected the boot loader and you cannot load Windows from the first drive, you can always boot from the Windows 11 USB and choose the Repair Windows option to make the first disk bootable again. But first check boot priority in BIOS. If the first disk is not first on the list, it could explain your issues. Make it higher priority than the second disk and see if it boots.

MisterEd · Tuesday at 10:29 AM

I use the free version of EasyBCD for configuring dual-boot. I installed Windows 10 on the 1st SSD and Windows 7 on the 2nd SSD. After this Windows 7 was the default that would boot automatically after 30 seconds. To fix this I used EasyBCD to make Windows 10 the default again.

BTW, one time the Windows 10 boot became corrupted so I couldn't boot to it. I repaired it by booting to the Windows 10 setup on a flash drive. After that Windows 7 was no longer on the boot menu. To fix that I ran EasyBCD and added Windows 7 back to the boot menu.

EasyBCD Main Menu

EasyBCD Edit Boot Menu

spapakons · Tuesday at 10:48 AM

I am not sure if EasyBCD works for UEFI boot entries. You might have to use EasyUEFI instead.

Celery · 2026-07-01T07:45:23-0400

Windows Setup automatically creates a UEFI boot entry in NVRAM (Non-Volatile Random-Access Memory) that points to \EFI\Microsoft\Boot\bootmgfw.efi on the EFI system partition. bootmgfw.efi is the Windows Boot Manager. It reads the Boot Configuration Data (BCD) store located on the same EFI system partition. The BCD determines whether Windows starts automatically or whether a graphical boot menu is displayed.

The difference between software-level and firmware-level boot management:

Windows Dual-Boot Menu: Shared EFI system partition

For example:
- Windows 11 On volume 3
- Windows 11 On volume 7

The "Change defaults or choose other options" link in the Windows 11 dual-boot menu (see image below) allows you to modify system startup behavior without logging in. From this screen, you can select which operating system loads automatically, change the boot wait time, and access advanced recovery options.

Motherboard one-time Boot Menu: Separate EFI system partitions

For example:
- Windows Boot Manager (Samsung SSD 970 EVO 2TB)
- Windows Boot Manager (Samsung SSD 990 PRO 1TB)

In your motherboard's boot priority settings (see image below), you can select which Windows Boot Manager entry the UEFI firmware starts by default.

Gigabyte X870E Aorus Master X3D Ice.webp

link626 said:
NVME1 and SSD2 each have their own efi partition. So why wasn't windows able to boot into NVME1 ?

NVME1 was removed and untouched during the installation of windows on SSD2.

I had to run the bcdboot command to fix nvme1.

Google Gemini:

When you have two completely independent drives, each with its own Windows installation and its own EFI System Partition (ESP), they should theoretically be able to boot independently via the motherboard's boot menu.

Here is why the OP's NVME1 drive failed to boot and required a bcdboot fix:

1. Disk Signature and GUID Clashing
When you install Windows on SSD2 while NVME1 is disconnected, Windows assigns standard identifiers to the new drive's partitions and the Operating System itself.

When you plug NVME1 back in, you now have two drives with identical Windows 11 layouts.

During the boot process, the motherboard initializes the hardware and hands off control to the EFI bootloader on NVME1.

However, once the Windows Boot Manager (bootmgfw.efi) starts loading, it scans the system's hardware to mount the Windows partition (usually C:).

If the Boot Configuration Data (BCD) on NVME1 references a disk signature or partition GUID that Windows confuses with SSD2, or if the drive ordering shifted in the BIOS after reinserting the NVMe drive, the bootloader tries to load the OS files from the wrong drive or partition. This mismatch triggers the Automatic Repair Screen.

2. NVMe Slot and Controller Re-initialization
NVMe drives interface directly with the PCIe lanes (either through the CPU or the motherboard chipset).

When the OP removed NVME1 and installed Windows on SSD2, the motherboard mapped SSD2 as the primary available bootable storage device.

Reinserting NVME1 forces the motherboard's UEFI/BIOS to re-enumerate the PCIe devices.

Some motherboards dynamically change the hardware path IDs or the hard drive BBS priorities when a drive is removed and re-added. If the BCD on NVME1 was looking for the OS at a highly specific hardware path that shifted slightly due to SSD2 being present, the bootloader will fail to find the Windows system files and crash into Recovery Mode.

Why did bcdboot fix it?
The bcdboot command forces Windows to rewrite the boot critical files and completely regenerate the BCD store from scratch.

By running this command, the OP forced the NVME1 bootloader to scan the current, exact hardware environment with both drives inserted, map the precise current volume GUIDs, and write a fresh, accurate path to the Windows directory.

Tip for Dual-Booting Independent Drives: It is highly recommended to disable Fast Startup in the Power Options of both Windows installations. This ensures that every time you shut down, the filesystems are cleanly unmounted and won't conflict when you swap between them using the motherboard boot menu.

Click to expand...

MisterEd · 2026-07-01T22:37:46-0400

spapakons said:
I am not sure if EasyBCD works for UEFI boot entries. You might have to use EasyUEFI instead.

I replaced the motherboard with one that supports UEFI so I decided to enable that when ready.

I converted the 1st drive with Windows 10 from MBR to GPT from the command line OK. That was not possible with the 2nd drive because it had Windows 7. With it I had to delete all the partitions and convert it from MBR to GPT using Disk Management in Windows 10. After that I booted into the BIOS and switched to UEFI. I then booted with the Windows 7 flash drive and installed Windows 7 on the 2nd drive.

At that point Windows 7 was the default O/S. I used EasyBCD to make Windows 10 the default instead.

According to NeoSmart I can use EasyBCD to add Windows 7 and 10 but I am out of luck with Linux. However, I still think I can install Linux Mint on the unallocated space on the 2nd drive. I just need to do some research and figure out how to do it.

If your Windows PC is booting in EFI mode, Microsoft has blocked the loading of legacy or non-Windows operating systems from the BCD menu. This means that you can no longer use EasyBCD to add Windows 9x, XP, or Server 2003 entries to the BCD bootloader menu. You also cannot add DOS, Linux, BSD, or Mac entries. You can add multiple Windows Vista, Windows 7, Windows 8, and Windows 10 entries; and you can also boot into BCD-based portable media, such as WinPE 2.0+ images.

EasyBCD and UEFI

Scott · 2026-07-02T00:21:30-0400

spapakons said:
I am not sure if EasyBCD works for UEFI boot entries.

It will pop up this message, but it still works fine.

spapakons · 2026-07-02T00:29:05-0400

Once I was experimenting with dual boot Windows and MacOS on a separate spare disk. When I removed the MacOS disk I had no way to remove the boot entry, there was no such option in my UEFI firmware (see my 2nd system specs). I had to use EasyUEFI to do it. However my Windows installation is MBR (Legacy BIOS), so EasyUEFI could not run. I had to boot a WinPE USB, such as Sergei Strelec WinPE in UEFI mode to run EasyUEFI from there. Running a standard UEFI mode installation of Windows 11 you should have no problem running both EasyUEFI and EasyBCD as needed.

why does bootloader always get messed up when dual boot installing on another drive?

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1. Disk Signature and GUID Clashing​

2. NVMe Slot and Controller Re-initialization​

Why did bcdboot fix it?​

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