How to Clone Your Windows OS from HDD/SSD to M.2 SSD for Free

I have 2TB HDDs and 120 GB SSD. I just want to transfer only my Windows OS from the HDD to the SSD and keep the rest of the files back on the HDDs, how do I do this safely without losing my files, applications, and settings?

If that sounds similar to your question, then keep reading as this post provides a step-by-step approach to accomplishing such migration safely.

There are several different ways of combining mechanical hard drives with SSDs to boost your Windows performance without blowing up your paycheck. Entirely replacing your slower, less efficient mechanical hard drives with a faster, more efficient SSD may appear to be the ultimate solution.

However, considering the cost implication of such an upgrade, one might be better off seeking a middle-ground for a more efficient and yet cost-effective solution, especially when there’s a need for a lot of storage space like the case in the question above.

The natural middle-ground for such upgrade and optimization would be to combine the less efficient mechanical hard drives with a faster, more efficient SSD.

Usually running your Windows operating system from the SSD and using the mechanical hard drive for storage. For someone who has been using only the mechanical hard drive for years, you would wish there was a magic wand for just moving your operating system to the SSD and keeping your files on the mechanical hard drive without having to reinstall your Windows or give up your applications and licenses.

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Well, wish no longer, here you will find step-by-step instructions on how to transfer only your operating system to the SSD and keep your files on the hard disk.  For this demo, I used the M.2 SSD the same exact approach would work for other SSDs as well.

Reasons Why You May Need This Solution:

  1. First is of course when you want to change from a mechanical hard drive to an M.2 SSD storage.
  2. Second is when you want to combine a mechanical hard drive with an M.2 SSD, normally using the SSD for your Windows and applications, and then the mechanical hard drive for storage.
  3. The third is when you want to upgrade from a smaller to a larger M.2 SSD especially if your laptop only has the M.2 socket for storage and you’re running out of disk space.

Just as we’ve seen with everything computing and electronics in general, the trend is constantly moving towards miniaturization of components, the hence smaller form factor for computers and gadgets. And as far as storage goes, the next phase we will be seeing will be wider adoption of the M.2 SSD storage.

Some manufacturers are already making for smoother transitioning by combining the traditional SATA connector and the M.2 connector on the same board, while others are already replacing the SATA connector with an M.2 connector completely.


To migrate your OS or entire disk to the M.2 SSD, here are the components you will need:

  • An M.2 to SATA adapter.  There are different forms of this adapter, this third one has a 2.5-inch enclosure, with that you can fully adapt the m.2 into the same compartment as traditional hard drives.
  • A USB to SATA adapter cable.
  • You could also get a USB to M.2 adapter to replace the two initial adapters, however, this adapter allows you to connect only through the USB port while using the other two allows you to connect both through USB and directly to a SATA interface.
  • Then you need a screwdriver for opening your hard disk bay, or laptop back cover depending on the kind of laptop you have.
  • And of course, your M.2 SSD. The size will depend on the space between your M.2 socket and the mounting post provided on your motherboard. So it could be the full height or the half-height M.2 SSD.

Before you go ahead to order any of the components, first check to see what you already have on your computer. Different laptop models provide you different kinds of connection interfaces, and for some laptops, you won’t even need any of these adapters, while for others, you might need one or two.

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For instance, this EliteBook 820 comes with two M.2 sockets.

One has the broadband card plugged to it, and the other is designed to hold the flash cache memory. However, both interfaces are able to support M.2 SSDs. The obvious bottleneck here is that the space between each of these sockets and the mounting posts are only long enough for the half-height M.2 SSDs. This does not mean that they can’t be used for cloning the full-height M.2 SSD. If all you want to do is to clone from your mechanical hard drive to an M.2 SSD, then you can attach the SSD to the connector, use a little strip of masking tape to hold it onto the frames, carefully place the laptop between two books or similar objects and proceed with the cloning process.

If however you want to combine the M.2 SSD with a mechanical hard drive in this scenario, then is best to use the half-height M.2 SSDs, this is not yet very common, but they are fast becoming more common as their storage capacities are getting higher, with both 128 GB  and 256 GB variants becoming more available.

So here with this setting, I will be able to move my Windows from the mechanical hard drive to the M.2 SSD and keep the mechanical disk for storage.

The second scenario is the case with this Acer Aspire 3.

This is a more recent design, here they provide a full capability for combining a mechanical hard drive with a full-height 80 mm long M.2 SSD. This is kind of the most ideal scenario for combining a mechanical hard drive with an M.2 SSD, here you don’t need any adapters and you will have a wider range of SSDs to choose from. This model also supports the NVMe technology, which is about 5 times faster than normal SSDs that are based on SATA 3.0 technology. So, if you use an M.2 SSD that supports NVMe on a laptop like this, then you can expect some really amazing performance.

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The third scenario is the case with this HP 250 G5, this model comes with only the M.2 interface.

so if I want to clone from a smaller 64 GB or 128 GB M.2 to a larger 256 GB M.2, then this solution could also come in handy for you. For this use case, you will need either the USB to M.2 adapter or both the M.2 to SATA and USB to SATA adapters. Here we need to attach the new M.2 SSD to this adapter. Then connect the adapter to a USB to SATA adapter cable and connect to the laptop.

With any of these three scenarios, the next step would be to download an OS migration tool, there are several of them online. The minitool partition wizard comes as a prime option for these operations is quite reliable and easy to use. It has a free version that can complete any of these tasks without limitations. The previous versions like Version 10.2  and Version 11.5 can offer you a complete migration for FREE if you follow the procedure showed in this tutorial and in the video below. The latest version, version 12 requires a paid pro subscription to perform disk cloning operations.

On this page, click on download and wait for the download to complete.

Run the installation by double-clicking.

Here select your preferred language and hit ok.

Accept the license terms and hit next on the following pages.

Here, choose whether or not you want to create a desktop shortcut and if you want to participate in the customer experience improvement program, then hit Next.

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On this next window, it asks if you want to install additional software. If you don’t, simply uncheck the box where it says “I have read the Privacy Notice…” and then hit Next to continue with the normal installation.

On the window that follows, hit Install.

Here, hit Finish to complete the process.

Before the next step, ensure your M.2 SSD is already connected to your laptop in case you’re using the USB SATA Adapter cable or any other connectors you have. In such cases if you have a USB 3.0 port, then you should definitely use it, this will fasten the process substantially compared to a USB 2.0 port.

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On this page, you want to choose the operation that is suitable for your need.

The first option which is Migrate OS obviously migrates only your operating system to the M.2 SSD. The second option which is  Disk Clone offers you a total migration of everything on your disk to the M.2 SSD. Including your operating system, applications, files, settings and so on. I had previously made a tutorial on this particular process using an earlier version of the minitool partition wizard, if that is what you want to do, then you can just click on this option and then follow the instructions here to complete the process. The third option is, of course, copying particular partitions to the M.2 SSD. To copy only your OS to the M.2 SSD, choose the Migrate OS option.

It then brings you to a page like this asking how you want to migrate your OS.

The first option here would be ideal if you want to completely replace your system disk with the M.2 SSD, but that’s not what I want to do here, instead, I want to move my operating system to the M.2 SSD and still keep the original hard disk in the computer for storage so I will choose this second option and hit next.

On this next page, it asks you to Select the Destination Disk.

This will be my new M.2 SSD which is disk 2, then hit next. It then reminds you that all the data on the destination disk will be destroyed, are you sure you want to continue? Here doublecheck that you have selected the right disk before hitting Yes.

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On this page, it shows a summary of all your selections.

By default, “Fit partition to entire disk” is selected and Disk 2 is the target disk, which is my M.2 SSD. If that’s right for you, leave the other options as default and hit Next.

It then informs you to configure your BIOS to boot from the destination disk when next you boot up, just click finish.

Next, it returns you to this main page below where you will now click apply on the top right corner to begin the migration process.

Here a note pops up recommending that I close all applications before applying the changes.

So close down your applications and hit ok to start the migration process.

If you get past this stage then just wait for the migration process to run as supposed.

However, oftentimes you will get this Notice saying operation copy partition cannot be completed because drive C is being used now, its okay to get this notice, mainly because some background processes running on your laptop makes your drive C appear too busy for the process, so it offers you three options, you either restart, retry or cancel the process, here I will choose Restart now and then wait for the partition wizard to automatically perform the migration process upon restarting.

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This process will take a while depending on how large your systems files are and also the performance of your laptop. With higher performance laptop in terms of your processor and RAM, this process could be a lot faster, but in any case, just be patient and wait for the migration process to complete.

Here I should mention that the OS migration process doesn’t delete your original system files from the mechanical disk or the source disk, it only makes a copy of your system files to the destination disk which in this case is the new M.2 SSD, so you will still be able to run only on your old disk if you choose to.

After the migration process, if we go to check the M.2 SSD from the computer folder, you will see that it now has similar files and folders as the mechanical hard drive, these are your Windows system files.

If for some reason your M.2 SSD doesn’t show up, then you will need to add it from the disk management settings. To do that go to your windows search and type “Create and format hard disk partition” and click on the corresponding result.

On this disk management page, you will see a disk that the size corresponds with the size of your M.2 SSD, but without a drive letter. Right-click on it and select change drive letter and paths.

Here click on add, then just leave the default letter and hit ok.

After a moment you should have your M.2 SSD showing in the computer folder.

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The final step would be to configure the BIOS to boot from the M.2 SSD instead of the mechanical hard drive. This process will differ depending on your PC model and the way your BIOS settings page is organized. The idea here is to change your boot priority order to start booting from the M.2 SSD instead of the mechanical hard drive. So from my BIOS, under advanced settings, I will go down to where it says Legacy boot order, move my M.2 SSD to the top of the boot order, then save and exit.

With that when next I boot up this laptop it will boot from the M.2 SSD instead of the mechanical hard drive.

NB: You will still be able to boot only from your old hard drive or SSD as this only makes a copy of your Windows OS on the M.2 SSD.

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Please share your comments, questions and feedback in the comment section below. 

The following video demonstrates the solutions in this tutorial.