Solved: Windows 10 Not Booting from Clonezilla Cloned Drive

User Case

Clonezilla is a partition and disk imaging/cloning program which helps you to do system deployment, bare metal backup and recovery. Many users use Clonezilla to clone disk on Windows 10. But some of them encountered some problems when using it, such as the above situation. How to fix this problem? Keep reading to find out.

How to Fix Clonezilla Cloned Disk Not Booting Issue

As showed above, you may encounter the problem of Clonezilla clone not bootable. The cloned hard drive won't boot issue is a common problem that has troubled numerous users. Before understanding its solution, you can first understand the cause of this problem. There are many causes of this problem, and I will list a few below for your reference.

✿ Set the wrong drive to boot from.
✿ The computer lacks the necessary drivers to boot up the cloned SSD, such as M.2.
✿ Disk partition style conflict, e.g. source disk - MBR, target disk - GPT.
✿ The source disk contains bad sectors, causing the cloned drive won’t boot.
✿ An incomplete clone (only cloned the system drive, the boot drive is not cloned).

Next, I will introduce you to 5 solutions to this problem, you can try the following solutions according to your situation:

• Solution 1. Change the Boot Drive in BIOS
• Solution 2. Install Drivers for Cloned Drive with DISM Command
• Solution 3. Convert Disk to MBR/GPT and Restart Cloning Disk
• Solution 4. Repair Windows Startup from Windows RE
• Solution 5. Run Bootrec.exe

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Solution 1. Change the Boot Drive in BIOS

The wrong boot device may cause Windows 10 not booting from the Clonezilla cloned drive. If you have more than one hard drive on your computer, it's a good idea to go into the BIOS and change the boot order to start from the cloned hard drive.

1. Restart your computer. When the startup screen appears, continuously press a specific key (usually F2, F8, F12, Del) to enter BIOS Setup.
2. Select Boot and choose the cloned hard drive as the first boot option.
3. Press F10 to save and exit the BIOS. Then restart the PC to check if it can start successfully.

Solution 2. Install Drivers for Cloned Drive with DISM Command

As mentioned earlier, the cloned drive won’t boot if Windows 10 computer lacks the necessary drivers. You can install necessary drivers with DISM Command.

1. Insert and connect the cloned disk correctly to your computer. Boot computer from Windows installation disc.
2. Open Device Manager (type device manager in the search box), expand IDE ATA/ATAPI controllers, right-click the listed controller and select Properties.

3. Check the controller type of the device, and then download the disk driver for the cloned disk.
4. Save the downloaded driver to a safe location on the device and remember its location.
5. Type command in the search box. Select the first search result and click Run as administrator.

6. Type the following command and hit Enter:

▶ Dism /Image:E: /Add-Driver /Driver:"Y:\Z.inf"

Tips✍:
● E - Replace E: with the drive letter of your Windows boot partition.
● Y - Replace Y: with the location of your downloaded disk drive.

7. After the process is complete, exit the Command Prompt.

After that, you can restart your PC and set the computer to boot from the Clonezilla clone disk to see if Windows 10 can boot successfully.

Solution 3. Convert Disk to MBR/GPT and Restart Cloning Disk

When your source disk is an MBR disk, the computer only supports BIOS Legacy boot mode. If your cloned disk is a GPT disk, the computer will not be able to boot from it. The reason is that GPT disks require UEFI boot mode. In addition, if the source system disk is GPT and the target disk is MBR, you also cannot make the cloned disk bootable.

The best solution for these two situations is to convert the target disk to MBR or GPT, keeping the new disk with the same partition style as the source disk. To do this, follow the steps below:

#1. Check The Partition Style of Both Source and Target Disks

1. Boot computer from Windows installation disc. Insert and connect the cloned disk correctly to your computer.
2. Open Disk Management (type disk management in the search box), right-click on the source disk, and select Properties. Then check the Partition style of your source disk.

3. Repeat Step 2 to check the partition style of your Colonezilla cloned disk.

#2. Convert Target Disk to MBR/GPT

If your source disk is with MBR but the new disk is with GPT, you'll need to convert the GPT disk to MBR. If the source disk is with GPT but the target is with MBR, convert the MBR to GPT. Here is an example of converting MBR disk to GPT disk.

Note✍: Before you convert a disk, backup any data on it and close any programs that are accessing the disk.

1. If the disk contains any partitions or volumes, right-click each and then click Delete Volume.
2. Right-click the MBR disk that you want to change into a GPT disk, and then click Convert to GPT Disk. Then you can restart cloning disk.

Solution 4. Repair Windows Startup from Windows RE

If you try to boot from the drive cloned by Clonezilla, but Window 10 not booting, you can try to repair Windows Startup in Windows recovery environment (Windows RE). The Windows Startup repair will fix some errors and help you boot successfully.

1. Boot from the Windows installation disc. Select Repair your computer.
2. When you get into Advanced options, select Troubleshoot -> Advanced Options -> Startup Repair. Then, it will start to repair the startup problem.

Solution 5. Run Bootrec.exe

If the Startup Repair does not resolve the issue, you can use the Bootrec.exe tool.

1. Boot computer from Windows installation disc. Select Troubleshoot -> Advanced Options -> Command Prompt.

2. In the pop-up Command Prompt, type the bootrec.exe command to launch this tool and fix the Windows 10 not booting with the following commands.

• bootrec.exe /fixmbr

• bootrec.exe /fixboot

• bootrec.exe /scanos

• bootrec.exe /rebuildbcd

Avoid Cloned SSD Won't Boot Issue with Clonezilla Alternative

Some of the above solutions are a bit tricky for people who do not understand computer technology skills. I recommend that you use the Clonezilla alternative to clone disk without any boot problems. AOMEI Backupper Professional, the best disk cloning software for Windows 11/10/8.1/8/7/Vista/XP, is embedded with the latest cloning technology and able to clone a hard drive to another drive in a fast, secure, and easy way. It offers:

✩ HDD/SSD Clone: Support a wide range of hard drives, including HDDs, SATA SSDs, NVMe M.2 SSDs, USB flash drives, and SD cards, etc.
✩ 2 Cloning Modes: Intelligent clone, Sector by sector clone. Its default cloning method, Intelligent clone, will only clone used sectors from one hard drive to another, while skipping bad sectors. Therefore, you can clone large HDD to smaller SSD.
✩ SSD Alignment: Improve SSD’s performance and prolong its lifespan if you clone to an SSD.
✩ User-friendly Interface and Simple Operation: It has a dark blue GUI. All operations are very simple, just a few clicks.

You can try to use it to clone the disk and boot from it without any boot problems. Click the download button below to install it on your computer. Then launch AOMEI Backupper, click Clone -> Disk Clone. Then select the source disk and target disk according to the prompts.

Note✍:
❂ If you just want to clone your Windows 10 system instead of all the data on the hard drive, select System Clone. It will automatically detect system-related partitions (such as C drive, system reserved partition, etc.), so you will not miss the cloning of "system reserved" partitions or other important files related to booting the computer.
❂ To clone a disk without an operating system, such as cloning an external drive or a USB drive, you can try free disk cloning software - AOMEI Backupper Standard.

To Sum Up

Hope you can solve the problem of Windows 10 not booting from the drive cloned by Clonezilla through the 5 solutions in this article. In addition to this problem, some users also reported that Clonezilla not working sometimes. In order to avoid any startup problems after the cloning process, I strongly recommend that you use AOMEI Backupper.

This software can also help you perform a bootable clone on Windows 11. Also, it has other powerful functions such as Backup, Restore and Sync. You can use it to create bootable media to help you successfully boot your computer when the system crashes. Have a try of this powerful software.