This article discusses the possible reasons for Clonezilla Windows 10 not booting from the cloned drive, along with corresponding solutions, and offers a simpler alternative at the end. Scroll down to learn more!
If your system refuses to start after cloning, you’re not alone. Clonezilla Windows 10 not booting is a common issue many users encounter after migrating OS to a new drive. While Clonezilla is a powerful and reliable disk cloning tool, the process doesn’t always guarantee a bootable result, especially if system partitions or boot settings aren’t copied correctly.
Users typically notice problems like a black screen with a blinking cursor, an “Operating System Not Found” error, endless boot loops, or even a blue screen during startup. These issues can be frustrating, particularly when the cloning process seems to complete successfully.
The good news is that most of these boot problems are fixable. With the right troubleshooting steps, ranging from adjusting BIOS settings to repairing boot files, you can get your cloned system up and running again without starting from scratch.
Understanding the root cause of boot failure after cloning with Clonezilla is key to fixing the issue quickly. In most cases, the problem isn’t the clone itself, but differences in disk structure, boot configuration, or system firmware.
If your cloned system won’t start, don’t panic. Here are some effective solutions, starting with checking the boot order and mode.
After cloning with Clonezilla, your computer may still be trying to boot from the old drive or another device. Ensuring the cloned disk is set as the primary boot device is often enough to resolve the issue.
Step 1. Restart your computer and enter BIOS/UEFI settings, usually by pressing F2, F12, DEL, or ESC during startup.
Step 2. Navigate to the Boot section. Locate your cloned drive or SSD in the list and move it to the top of the boot order.
Step 3. Press F10 to save changes and exit. Once done, your system will attempt to boot from the cloned drive first.
Another common reason for Clonezilla Windows 10 not booting is a mismatch between partition style and firmware mode. If your source disk used GPT, the system should boot in UEFI mode. If it used MBR, it should boot in Legacy (CSM) mode.
Step 1. Restart your computer and access the BIOS/UEFI settings.
Step 2. Locate the Boot Mode, UEFI/Legacy Boot, or CSM Support option (varies by manufacturer). Then, change the boot mode:
Step 3. Save the changes and exit BIOS/UEFI. Your system should be able to recognize the cloned disk and boot into Windows 10 successfully.
If your system still won’t boot after cloning with Clonezilla, the bootloader may be missing or corrupted. You can repair it using the Windows Recovery Environment (WinRE), which rebuilds essential startup files like the Boot Configuration Data (BCD).
Step 1. Boot your computer using a Windows 10 installation USB/DVD.
Step 2. Click Next on the setup screen. Then, select Repair your computer instead of installing Windows.
Step 3. Go to Troubleshoot > Advanced options > Command Prompt. In the Command Prompt windows, enter the following commands one after another:
Step 4. Restart your computer and check if Windows 10 boots normally.
Step 5. If not, usually under Windows Boot Loader, the device and osdevice are displayed as unknown. Enter the Command Prompt window again and type bcdedit /enum to check this.
Step 6. Copy the correct {identifier}, usually {current}, {default}, or a GUID, and run the following commands. Restart again.
On GPT disks, Windows relies on the EFI System Partition (ESP) to store critical boot files. If this partition is missing, damaged, or improperly configured after cloning the hard drive with Clonezilla, your system won’t boot. Rebuilding the EFI partition can restore normal startup.
Step 1. Boot from a Windows installation and then open Command Prompt.
Step 2. In the Command Prompt window, type diskpart and press Enter.
Step 3. To identify EFI partition and assign a drive letter, type:
Step 4. To rebuild EFI boot file, type:
bcdboot C:\Windows /s Z: /f UEFI
Step 5. Type exit to close the Command Prompt window and restart your computer.
Once completed, the EFI partition will be recreated with the correct boot files, allowing Windows 10 to boot properly from the cloned GPT disk. If it is still not working, try:
If your cloned disk uses MBR and still won’t boot after using Clonezilla, the system partition may not be marked as Active. In MBR-based systems, only the active partition can boot Windows 10, so this setting is critical.
Step 1. Boot from Windows installation media and open the Command Prompt.
Step 2. In the Command Prompt window, type diskpart and press Enter to start DiskPart.
Step 3. To identify the correct partition and activate it, type:
Step 4. Exit DiskPart and restart your computer. Once activated, the system BIOS will recognize it as bootable, helping Windows 10 start normally.
While Clonezilla is powerful and widely used, many users eventually look for simpler alternatives, especially when dealing with boot failures like Windows 10 not booting after cloning. In many cases, the goal is not just to copy data, but to ensure the cloned drive boots correctly without additional repair steps.
When choosing a disk cloning tool, especially to avoid boot issues, look for solutions that simplify the process and minimize manual troubleshooting. AOMEI Cloner is a good choice because of its user-friendly design and powerful cloning features.
Step 1. Connect your new hard drive or SSD using a compatible adapter. Download and install AOMEI Cloner on the Windows 10 computer. Open AOMEI Cloner after installing and click Clone > Disk Clone to get started.
Step 2. Select your Windows 10 system drive as the source drive and the new hard drive or SSD as the destination drive. Click Next after each selection.
Step 3. It will automatically resize the target drive to full capacity (if it’s large). You can click Edit Partitions to confirm this. Meanwhile, check the option to convert disk type (from MBR to GPT or vice versa) if the two disks are of different types. At last, click Start Clone.
For an SSD disk, it’s suggested to enable SSD Alignment for high performance.
Using Sector by Sector Clone may cause Clonezilla clone larger disk to smaller disk to fail. Don't check this option.
After cloning, perform a boot test to ensure the cloned drive will boot successfully.
Clonezilla Windows 10 not booting from cloned drive is usually caused by bootloader errors, partition mismatches (MBR/GPT), incorrect BIOS/UEFI settings, and most problems can be fixed. It’s advisable to start by adjusting boot order, switching boot modes, and then repairing or rebuilding boot files.
In addition, the easiest method to fix this issue is using an easier alternative, and we recommend using AOMEI Cloner, a powerful cloning software designed to clone Windows 10 hard drive, effectively addressing all types of cloning issues.