Why Windows Server 2012 Hard Drive Space Disappearing and How to Fix?

September 12, 2017

Do you know why your hard drive space missing on Windows Server 2012/2008/2003? Let’s find out lost space and make some change to avoid follow-up bad effect on Server.

The Scenario

“Please help. My Windows Server 2012 hard drive space disappearing slowly when there is no files add in. Here is the thing, my C drive with 80GB in size showed as have 1GB free. However, when I check files in Windows File Explorer, the total size of used space is not that much. Why could this happen? It is so weird and I am in the worry of affecting my system running and software installation. Any advice would be appreciated.”

This is a common issue that happened on Windows Server 2012 (R2), Windows Server 2008 as well as Windows Server 2003. Windows Server 2012 shows incorrect disk size and loses hard drive space for no reason. Don’t worry, following paragraphs will tell you what takes up your disk space and how to find them.

Where is the lost disk space on Windows Server 2012?

First of all, you need to know that the space is not really missing. The disk capacity keeps unchanged on the hard drive and is occupying by files. However, for some unknown reasons, they are invisible so that you cannot see them. Generally speaking, there are four factors account for the phenomenon.

Different calculate methods on disk usage

Windows actually has two methods used for calculating disk usage, Volume Bitmap Analysis and File Scanning with FindFirstFileEx /FindNextFile. Volume Bitmap Analysis retrieves a bitmap of occupied and available clusters on a volume, and FindFirstFileEx function searches a directory for a file or subdirectory with a name and attributes that match those specified.

That is to say, files calculated by Volume Bitmap Analysis may not be calculated by FindFirstFileEx function. As a result, you’ll see different disk space size on used and free. That makes disk space missing on Windows Server 2012 understandable. Well, what kind of files can’t you see in Server File Explorer?

Hidden files on the hard drive

In order to ensure Server OS running normally, Windows set some files as “hidden”, which prevent system files from to be deleted mistakenly and causes system meltdown. In Server 2012 File Explorer, go to “View” and check “Hidden items” option to make the hidden files appear. You can easily tell that “ProgramData” folder was hidden before.

Hidden Items

Memory dumps on system drive

In “\Documents and Settings” or “\users” folder, you can browse all the profile folders on the system disk. You need administrative permission to open these files. Otherwise, you may get “Access Denied” error. Chances are that these files are years of memory dumps, MP3’s, VHD’s, PDF’s, etc. You can check the number of files and the size on disk for all files in that folder and add it to the total.

System Restore Points are taking up the space

System backup enables shadow copy and creates system restore points (i.e. previous versions of system). By default, the backup is set to take up 50% of disk space and places the system images along with C drive. Head to System > System Protection > System Protection Tab > click on the C drive in Protection Settings and then the Configure to see how much space is being used.

If you have made regular backups for your Server 2012 (R2), it is suggested to delete these images and disable system backup to free up disk space. Absolutely, there are many other causes for hard drive space disappearing on Windows Server, like temp files of some installed third-party software. Run “Disk Cleanup” will free up disk space as well. You can visit Windows Server 2012 C drive out of space for detailed steps with screenshots.

Tips: Above elements apply to disk space missing on Windows Server 2003/2008 as well. 

Well, after knowing what takes up your hard disk space, you won’t feel that Server 2012 is losing hard drive space for no reason. In some cases, the file that occupying disk space cannot be deleted or moved to another drive. Thus, to ensure system works well and does not affected by low disk space on the C drive, you might as well re-adjust the partition size on the hard drive.

Manage hard drive space on Windows Server 2012 reasonably

AOMEI Partition Assistant Server allows you to resize hard drive partition to the state you wish. More importantly, it requires no unallocated space for extending a partition. The “Allocate Free Space” feature will add redundant space from one partition to another without shrinking first. Resize all partitions to a reasonable state if necessary.

Resize partitions to allocate disk space in reason

Open AOMEI Partition Assistant. At main interface, you’ll have a brief understanding of your hard drive partition state. Do the resizing based on your needs. This guide will take extending C drive with the space from data partition for example to solve Server 2012 disk space disappearing.

Step 1: Right click on the partition that has redundant disk space and select “Allocate Free Space”.

Allocate Free Space

Step 2: At the pop-up page, specify the size of free space you want to allocate and select C drive as the destination.

Space from E to C

Step 3: Preview the outcome and click “Apply” > “Proceed” to execute the pending operations.


It will reboot to complete the process since the system drive is involved in. In quite a few cases, the process may be hanging even if it is completed. Just reboot your computer manually and you’ll find that the C drive has been extended.

Tips: with this feature, you can reallocate free space to different partitions if you have many partitions on the hard drive. 

Upgrade small hard drive to a larger one

In some cases, the Windows Server 2012 hard drive has small capacity. When realized that the file which taking up disk space cannot be deleted, you may need to upgrade to a bigger disk to accommodate all of them. Then, the Server OS effective running could be guaranteed. Prepare a larger disk and you can achieve the goal with the same tool, AOMEI Partition Assistant Server.

Copy Disk Method

  1. Connect the new hard drive to your Server 2012 (R2) and be sure it is detected. Start AOMEI Partition Assistant and click on “Disk Copy Wizard”. Then, you have two methods to copy the disk. Choose the one that suits you and continue.

  2. Select current hard drive as the source.

  3. Select the new disk as the destination. If copy hard drive to SSD, please check “Optimize the performance of SSD” option.

  4. (Optional) You can edit partition size and drive letter if you select “Copy Disk Quickly” method before.

  5. An important note about booting up from cloned hard drive. You may want to keep it in mind.

  6. Now, click “Apply”>“Proceed” to submit the order.


  • The process will be finished after restarting system.

  • These solutions work for Server 2008/2003 disk space disappearing on both laptop and desktop as well.


Windows Server 2012 hard drive space disappearing might be caused by different causes, but what counts next after knowing what is occupying the disk space is to fix them with reasonable solutions. With AOMEI Partition Assistant, you can manage your hard drive better. For example, you can mirror MBR HDD to GPT HDD on Server 2012 without formatting.