Windows Server 2016 Repair Boot | 2 Effective Solutions

Do you get stuck in Windows Server 2016 boot failure and desire to figure out how to repair it? Learn how to repair Server 2016 with Command Prompt and a powerful backup and restore tool from this page.


By Lily Updated on December 14, 2023

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The issue: Windows Server 2016 won’t boot

Windows Server 2016, developed concurrently with Windows 10, is the successor to Windows Server 2012 R2. It features Nano server which is so small that it doesn't have any direct user interface besides the new Emergency Management console. It also features Windows Server and Hyper-V container, and Linux secure boot, etc.

Windows Server 2016

Superb as it is, some users find Windows Server 2016 won’t boot after update. And there are users who receive an error message, “Windows failed to start. Status: 0xc000000e” after a full OS recovery. How does the error occur? This problem could be caused by the errors or damage on server boot files or even system failures. Then, how to run Windows Server 2016 recovery?

Based on different causes, you can choose to run the Bootrec.exe tool in the Windows RE or try Windows Server 2016 restore from backup if you backed up Windows Server 2016 before. These methods will be specifically described below.

👉 Way 1. Repair Windows Server 2016 with Bootrec.exe
👉 Way 2. Run Windows Server 2016 recovery via AOMEI Backupper.exe
👉 Bonus tip: Best enterprise data backup solution

Way 1. Repair Windows Server 2016 with Bootrec.exe

This method applies to Windows Server 2016 repair boot:

1. Insert the Windows Server 2016 installation media into your computer and boot from it.

2. At the Windows Setup Dialog, set your appropriate settings and click Next.

3. Click Repair your Computer > Troubleshoot > Command Prompt.

Repair Your Computer

4. In Command Prompt, input following command lines and press Enter after each.

  • bootrec /fixmbr

  • bootrec /fixboot

  • bootrec /rebuildbcd

  • y (to confirm that you want to add new Windows installations to the Boot Configuration Database)

5. Exit Command Prompt and restart your computer.

Way 2. Run Windows Server 2016 recovery via AOMEI Backupper.exe

If the Windows Server 2016 boot issue is caused by system failures, AOMEI Backupper Server comes to help. Especially designed for small and medium sized business, it is your total data protection and disaster recovery solution. Following are its main features:

Backup all kinds of data
It offers you four backup types that enable you to create backups for the server system, whole disk, specific partitions, or individual files.
Backup based on a schedule 
It allows you to perform automatic backups. You can set a backup task to run daily, weekly, monthly, or based on events (user logon, user logoff, system startup, and system shutdown), etc.
Delete obsolete backup versions
AOMEI Backupper is a wonderful backup disk space manager. It can delete old backups automatically with the inbuilt deletion mechanisms.
Flexible and quick restore
You can restore system, disks, partitions, or files easily from the backup images you created before, either through GUI operations or command lines. You can even restore system to dissimilar hardware via "Universal Restore".

Before running a system restore:

  • If you own a good backup habit and have already made a system backup via AOMEI Backupper, you can try Windows Server 2016 system restore in following steps. 

  • If you haven’t created a system backup with AOMEI Backupper, you can create one on another computer running Windows Server 2016. However, your computer will be restored to the state of the computer where the system backup is made.

  • You may use AOMEI Backupper Check Image utility to check if the system backup image is intact and without error. 

Now let’s get straight to Windows Server 2016 repair:

1. Create bootable media with AOMEI Backupper on a computer functioning well.

Create Bootable Media

2. Boot the computer which has a boot problem from the bootable media. You’ll see loaded AOMEI Backupper once login. Go Tools > Windows shell command to open Command Prompt.

Windows Shell Command

3. Type cd C:\Program Files (x86)\AOMEI Backupper and press Enter. You should change the path after “cd” with the installation directory of AOMEI Backupper on your computer.

4. Type AMBackup /r /t system /s “D:\systembackup\systembackup.adi” /d 2 to restore the system backup saved in D:\system backup to disk 2 and press Enter. You should change the path of the image file and the destination location with yours.

5. Type exit to exit Command Prompt and press Enter. Restart your computer later.

AOMEI Command Line

Note: The drive letters might change under Windows PE environment. You can run AMBackup /l before Step 4 to list disks on your computer and type disk number after AMBackup /l (ex: AMBackup /l0) to list partitions on a specific disk.

How to do Windows Server 2016 system restore in GUI

Some users prefer GUI operations to repair Windows Server 2016. AOMEI Backupper Server can also meet the demand:

Step 1. Create bootable media and boot from it as mentioned above.

Step 2. When you see loaded AOMEI Backupper, select “Restore” on the left pane and tick “Select Task” to show backup tasks.

Select Task Winpe

Step 3. Select the system backup task in the list and click “Next”.

Select Backup Image

Step 4. Select to restore entire backup or a part and click “Next”.

Restore Entire Backup

Step 5. Confirm operations on the “Operation Summary” page and click on “Start Restore” button.

Preview Restore


  • If the size or location of the original system drive has changed, you will need to specify the destination drive before Step 5; if not, the program will automatically select the current system partition (usually C drive) as destination drive. You can also change the default destination drive by ticking before “Restore system to other location” in Step 4.

  • If your system backup image is from another computer, you should tick “Universal Restore” in Step 5 to ensure the system is bootable after recovery.

Bonus tip: Best enterprise data backup solution

If you are an enterprise user who has multiple Windows Server devices that need to be backed up, you can try the best enterprise backup software - AOMEI Cyber Backup. It offers you all-around enterprise data backup solutions:

  • It enables you to create system/disk/partition backup for a bunch of Windows PCs and Servers, supporting Windows 11/10/8.1/8/7 and Windows Server 2022/2019/2016/2012 (R2)/2008 (R2).
  • You are allowed to save backup images on a local disk, external hard drive, network share or NAS device, etc.
  • You can schedule a backup task to run every day/week/month using the full/incremental/differential backup method.

Download this powerful enterprise backup software now to have a try!

Download Free TrialEasiest Enterprise Backup Software
Secure Download

To make backups for client computers, just log in AOMEI Cyber Backup, and add the Windows device that you want to backup. Then click Backup Task on the left menu bar and select Backup Task Create New Task.

Create New Task

Note: AOMEI Cyber Backup can not only help you backup physical machines but also virtual machines. It enables you to backup VMware and Hyper-V easily.


When you encounter Windows Server 2016 boot error, you can either run the Bootrec.exe tool to fix boot or use AOMEI Backupper Server for system restore. Windows Server 2012 repair boot can be achieved in the same ways. What's more, AOMEI Backupper offers the clone feature to help you clone Windows Server 2016 to SSD.

To protect unlimited PCs and servers within your company, you may choose AOMEI Backupper Technician Plus. You will be surprised to find that it enables you to copy the installation directory for portable version creation. Don't hesitate to try it out!

Lily · Editor
Lily Green joined AOMEI in 2018 and has since become a professional in the areas of data protection and data transfer. She is committed to helping users protect their precious computer data and troubleshoot Windows system errors. She consistently stays vigilant about the latest trends in technology, guaranteeing that the given information aligned with the ongoing advancements in the field.