Repair Windows Server 2016 “BootMgr is Missing” Boot Error

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By Victor Ashiedu

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If your Windows Server 2016 is broken, you may need to repair its boot record. Here are 3 methods to fix Server 2016 boot errors.

Step 1: Boot to Recovery Mode

The 2 options discussed in this guide require you to boot your server to recovery. For each method, I will refer you to this link – Boot to Windows Server 2016 Recovery Mode Without Installation Media (DVD or USB).

Use the steps described in the link above until you get to the Choose an option screen shown below. Then proceed with the remaining steps in each method.

windows server 2016 repair boot

Step 2 (Option 1): Rebuild the Boot Configuration Data (BCD)

The first option for Windows Server 2016 Repair Boot is to rebuild the BCD.

Here are the steps:

  • At Advanced options, click Command Prompt.
windows server 2016 repair boot
  • To open Command Prompt, choose an account with admin privilege. In this example, I will click Administrator.
windows server 2016 repair boot
  • Finally, type the password for the account. Then click Continue. Command Prompt will open.
windows server 2016 repair boot

In the next steps you will run some commands that will repair your server’s Boot Configuration Data (BCD). This commands will fix corrupt boot configuration data.

There are two sets of command options below: 1, commands to use if your computer has BIOS with MBR systems. 2, commands applicable to UEFI systems

Commands to Repair Boot (Rebuild BootMgr) for MBR Systems

If your computer uses MBR, follow the steps below to repair Server 2016 boot records:

  • At the previous command prompt, enter the following commands one at a time. Then press enter at each command.
bcdedit /export C:\BCD_Backup
attrib c:\\boot\\bcd -h -r –s 
ren c:\boot\bcd bcd.old
bootrec /rebuildbcd  

When the last command completes, you will receive this prompt:

Add installation to boot list? Yes/No/All:

Type A and press enter.

Steps to Repair Server 2016 Boot for UEFI systems

If your Server runs the new UEFI use the steps here for Windows Server 2016 repair boot:

This section has two parts: part 1, use diskpart to assign a drive letter to the EFI volume. part 2, rebuild BCD.

Here are the steps:

  • At the command prompt type the command below. Then press enter
DISKPART

The last command will open dsiakpart command prompt.

  • At the DISKPART prompt, type this commend and press enter
LIST DISK

All available disks on your Server will be displayed.

  • Next, to select the disk with your Windows Server 2016 installation use the command below:
 SELECT DISK 0 
If your operating system is installed in a disk with a different number, change 0 to that number in the previous command. The command will return the result below:
  • To display available volumes in the selected disk, type the command below. Then press enter.
LIST VOLUME

Before you proceed to the next step, you need to identify the EFI volume

Here is how you identify the EFI volume:

  1. It should be formatted with FAT32
  2. Size is likely to be about 100mb (shown as 99mb in this example)
  3. The volume may likely show as hidden

To select the EFI volume, run a command similar to this command:

SELECT VOLUME 3

Replace 3 with the # for your EFI volume

  • Finally for this part, assign the volume a drive letter with this command:
 ASSIGN LETTER K:

When you run the last command, you should receive “DiskPart successfully assigned the drive letter or mount point”. If you receive any other message, repeat the last command with a different drive letter.

  • To exit DISKPART, use exit command.
EXIT
windows server 2016 repair boot

You will be returned to Command Prompt. DO NOT close it as you will need it in part 2 of this section.

Here is the second part for Windows Server 2016 repair boot (Repair BCD):

  • At the command prompt, change directory to point to the EFI boot drive. Use the command below:
 CD /d k:\efi\microsoft\boot\ 

K: is the drive letter you assigned the EFI volume. See the result of the command below:

windows server 2016 repair boot
  • Finally, execute the following commands one at a time:
bcdedit /export K:\efi\microsoft\BCD_Backup 

The command creates a backup of the boot configuration data (BCD). Just in case you need to restore it!

ren bcd bcd.old 

It renames the current BCD to bcd.old. Finally, to rebuild BCD and repair Windows Server 2016 boot, use this command:

bootrec /rebuildbcd 

The last command will take a short while to complete, then it will return prompt for confirmation –

Add installation to boot list? Yes/No/All:

Type A and press Enter.

  • Exit command prompt. Then click Turn off your PC.

From my experience, the fix you just went through will repair Windows Server 2016 boot.

But if in the rare instance that your server still cannot boot, try the next fix…

Step 2 (Option 2): Restore to a Previous System Restore Point

To use this method you must have enabled system restore and created a valid restore point before your server crashed. If your server do not have a restore point, use Rebuild the Boot Configuration Data (BCD) method.

Here are the steps for this fix:

  • At Advanced options, select System Image Recovery. Then follow the wizard to revert your server to a previous restore point.

Frequently Asked Questions

1. How do I run a repair on Windows Server 2016?

Boot to Windows Server 2016 Recovery Mode (link opens in a new browser tab). When you get to Choose an option, click Troubleshoot -> Command Prompt. Then, use the following methods to run a repair on Windows Server 2016:

1. Rebuild the Boot Configuration Data (BCD)
2. Restore to a Previous System Restore Point

For the detailed steps for the 2 methods, read this guide from the beginning.

2. How do I boot Windows Server 2016 to Startup Repair?

To boot Windows Server 2016 to Startup Repair:
1. Power up the server by pressing the power button. Wait for the Windows Server to initiate boot – the Windows logo is displayed or some circles are displayed. Then, press and hold the power button until the server powers off.
2. Repeat step 1 for the second time
3. When you power up the server for the third time, it will boot Startup Repair.

3. What is Bootrec RebuildBcd?

Bootrec.exe is a Windows Recovery Environment command-line tool used to fix Windows boot problems. The /RebuildBcd switch scans all disks for Windows installations. Then, if it finds a Windows installation, it prompts you to add the installation to the boot list. Effectively, the Bootrec /RebuildBcd command rebuilds the Windows Boot Configuration Data (BCD).

4. Why is Startup Repair taking so long?

One reason Startup Repair may take too long is if the repair process is stuck. If this happens, simply press and hold the power button to force a restart. If this does not fix the problem, your Windows installation may be badly corrupt and Startup Repair is unable to fix the problem. If this happens, boot the computer to Startup Repair and select Command Prompt, then on command prompt, execute the following commands:

bcdedit /export C:\BCD_Backup
attrib c:\boot\bcd -h -r –s
ren c:\boot\bcd bcd.old
bootrec /rebuildbcd

5. Is Windows Server 2016 part of Windows 10?

The simple answer is, No. Windows Server 2016 is a Windows Server Operating System while Windows 10 is a Windows client Operating System. A Server Operating System is used by network administrators to manage multiple users in the network while a client Operating System like Windows 10 is installed on individual laptops, or desktops and used by a single person.

Conclusion

The first fix in this guide is likely to resolve Windows Server 2016 boot problems. But if it doesn’t and you have a restore point you may try the second method.

I am confident that one of the methods will get your server up and running.

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Did you find this fix useful? For Windows server fixes, visit our Windows Server Fix page.

About the Author

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Victor Ashiedu

Victor is the founder of InfoPress Media, publishers of Ilifeguides and Itechguides. With 20+ years of experience in IT infrastructure, his expertise spans Windows, Linux, and DevOps. Explore his contributions on Itechguides.com for insightful how-to guides and product reviews.

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