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My setup is windows 10 installed on a SSD, and then 2 other hard drives. I attempted to convert the SSD to GPT(I think that is correct) for windows 11 installation. I got the error message "The system partition and boot partition are separated on different disks."

Looking for any advice.

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  • A screenshot of Windows own Disk Management would probably gives us more info. Anyway, the message is probably sort of bogus. It may probably be just that the tool does not how to handle things when there isn't a dedicated boot partition, which means it can't simply replace it with an EFI system partition (ESP). You may consider shrinking the main partition yourself, then create an ESP with e.g. diskpart and install the UEFI Windows Boot Manager to it with bcdboot. Then convert only the partition table style with some other tool (gdisk on Linux or whatever).
    – Tom Yan
    Commented Dec 22, 2022 at 4:38
  • imgur.com/a/RTCMLGa Here is a picture of it. sorry.
    – Jen
    Commented Dec 22, 2022 at 5:10
  • Hmm okay. Seems that your current Windows Boot Manager is indeed on Disk 1 / one of the HDD. But the suggestion / instruction I've given stands anyway.
    – Tom Yan
    Commented Dec 22, 2022 at 6:01
  • Thank you, I am a not as much of an expert, can i get a bit easier steps on how to do it. Can I use the AOMEI application to help me do it? really appreciate it.
    – Jen
    Commented Dec 22, 2022 at 6:31

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This is probably a case of the computer booting into one of the hard drives, and the bootloader on that drive loads Windows from the SSD - which is obviously not a good idea. You will need to change this so the computer boots directly from the SSD.

Try doing the following -

  1. First, check if the SSD happens to have a valid (but unused) boot partition. Pull the two hard drives out of the computer, keeping only the SSD, and try booting your computer. If Windows works fine then reconnect the hard drives, go into the BIOS settings and change the boot order so it only boots from the SSD and not any of the other hard drives. You should be fine at this point.

  2. If the computer does not boot, go into the BIOS settings and verify that the SSD is on the boot device list. Add it if it isn't. Also there is a boot device selection menu that can be accessed by pressing a certain key during startup (It's usually F9, F12 or ESC) which can force your computer to boot from a specific device. If you manage to boot Windows that way then again this is easily solved by changing the BIOS boot settings.

  3. If you still can't boot Windows it means that unfortunately the SSD does not have a valid MBR / Bootloader and you will need to install it. Fortunately you do not need to completely reinstall Windows. Still, before going any further BACKUP ANY AND ALL IMPORTANT DATA. There is always a chance of something going wrong ending with the computer being unable to boot.

  4. You will need the Windows 10 installation media (on DVD or USB drive). If you don't have it then you can download it from Microsoft (use the Media Creation Tool).

  5. Here's a short guide on how to use the installation media to repair the bootloader. Keep the two hard drives disconnected when you do this. https://neosmart.net/wiki/fix-mbr/#Fix_the_MBR_in_Windows_10

  6. After repairing the bootloader Windows should boot properly. Reboot your computer and make sure it does. Then reconnect the two hard drives and change the BIOS settings so it boots only from the SSD.

  7. You should be able to convert to GPT at this point. Please make sure that your computer has UEFI firmware before you do. If it's an old computer that has a legacy BIOS it will not be able to boot from GPT and since this is a one way process you will need to reinstall Windows to fix your computer.

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