How to Clone Dual Boot HDD to SSD (Windows + Windows)

Why cloning dual boot drives is tricky?

Cloning a dual boot drive isn’t as simple as copying everything over. Here’s why it can get complicated:

📍 More Than One Partition

Dual boot systems have multiple partitions—one for each OS, plus boot and system files. Miss one, and your system might not start.

📍 Two Bootloaders, One Job

Windows uses its own bootloader, and Linux often uses GRUB. If the bootloader doesn’t copy correctly, you might only be able to boot one OS—or neither.

📍 BIOS vs UEFI Settings

Your HDD might be using BIOS (MBR), while your SSD defaults to UEFI (GPT). If these don’t match, your computer may not recognize the new drive.

📍 Windows Gets Confused

If disk IDs or drive letters change, Windows can fail to boot or behave oddly after the clone.

📍 Boot Files May Still Point to Old Drive

Even if the clone works, your system might still try to boot from the HDD—until you fix the boot configuration.

Best software for dual boot cloning in Windows

When cloning a dual boot system, the right tool makes all the difference. You need software that can handle multiple partitions, preserve bootloaders, and copy everything exactly—without skipping over essential system data. For Windows users, AOMEI Cloner stands out as one of the best options.

Download AOMEI Cloner and install it on your PC now.

Note: If you are using Windows + Linux setup, please turn to a tool that supports both Windows and Linux, such as Clonezilla.

How to clone a dual boot hard drive to SSD

Before you clone dual boot HDD to SSD, please get your SSD prepared:

• Connect your SSD via SATA, NVMe, or USB (using an adapter or enclosure).
• Make sure the SSD has enough space to hold everything from the HDD.
• Back up important files on the target SSD to avoid data loss after cloning.

Then, follow the instructions below:

Step 1. Launch AOMEI Cloner. Then go to Clone > Disk Clone (not “System Clone”—that only copies one OS).

Step 2. Select your dual boot HDD as the source disk. Click Next to continue.

Step 3. Choose the SSD as the destination disk and click Next.

Step 4. Tick SSD Alignment to improve SSD performance and lifespan, then click Start Clone. The process can take a while depending on disk size and speed.

Test your SSD setup after cloning

Once you've cloned your dual boot drive to an SSD, the next step is to make sure everything works as expected. Testing both operating systems and verifying performance ensures your clone was successful—and your system is stable going forward.

1. Boot from the SSD

• Restart your computer and enter the BIOS/UEFI setup (usually by pressing F2, F10, Del, or Esc at startup).
• Set your SSD as the primary boot device.
• Save changes and reboot.

💡 If both OSes show up in the boot menu or start normally, you're off to a good start.

2. Test Each Operating System

Boot into each Windows and make sure it loads fully. Check that programs, files, and settings are intact.

If either OS fails to boot, you may need to repair the bootloader:

Ⅰ. Boot from Windows recovery media and go to Troubleshoot -> Advanced Options -> Command Prompt.

Ⅱ. Type the following commands and press Enter after each line:

• bootrec /fixmbr
• bootrec /fixboot
• bcdboot C:\Windows (replace “C:\Windows” with the path to the unbootable Windows)

3. Check Partition Layout

Press Win + X and select Disk Management. When Disk Management opens, verify that all expected partitions are on the SSD.

4. Remove or Wipe the Old HDD (Optional)

Once you confirm everything works, you can either format the old HDD and use it for storage or remove it entirely to avoid boot conflicts.

💡 Just be sure not to boot from the old drive again, or you might accidentally confuse the system.

Summary

Cloning a dual boot HDD to an SSD can boost your system’s speed without reinstalling OSes. While it’s a bit more complex than cloning a single OS, using reliable software like AOMEI Cloner makes the process smoother. This guide walks you through the process of how to clone a dual boot hard drive to SSD and how to test the setup. With careful cloning and the right settings, your dual boot setup will run faster and cleaner on an SSD.