How to Repair Boot.ini for Windows Server 2012 (R2)?

Overview of Windows Server Boot.ini files

In Windows Server 2012, the traditional boot.ini file used in older systems has been replaced by the Boot Configuration Data (BCD) store, a database that manages boot-time configuration. Located on a special hidden partition of the system drive, the BCD helps Windows manage boot options, such as operating system selection, advanced settings like Safe Mode, memory configurations, and even dual-boot setups.  If the BCD becomes corrupted, it can prevent the system from booting properly, causing errors like "Boot Configuration Data file is missing."

How to repair boot.ini for Windows Server 2012(R2)

To fix this issue, you can use Windows installation media to run Startup Repair or manually rebuild the BCD by entering the command bootrec /rebuildbcd. Another option is to use a tool like AOMEI Partition Assistant, which helps repair or adjust BCD entries to restore correct boot settings if they are damaged. Keeping the BCD in good shape is important for making sure the server starts up reliably.

Method 1. Repair the boot.ini file for Windows Server 2012 with CMD

If you have a Windows installation disc or repair disk available, follow the steps in the first section. If you don’t, please check the next section for other options. Now, insert the installation disk into your machine and start it up. Then, follow these steps to rebuild the BCD for your Windows Server 2012.

Step 1. At the installation interface, choose language, time and keyboard input, and then click Next.

Step 2. Click on "Repair you computer" in the lower left corner.

Step 3. Go "Troubleshoot > Command Prompt" to start CMD. Then, type "bootre /rebuildbcd" and hit Enter. Wait for the process completes.

Step 4. Close the command prompt and back to the Choose an option interface. Click on "Continue". It will prompt to press any key to start. Press any key to restart your Server. The BCD file should be rebuilt and the Server can start properly.

If that does not work, type following commands first and then rebuild the BCD file.

bootrec /fixmbr

bootrec fixboot

bootrec /scanos

If your Windows Serve 2012(R2) failed to boot, fixing a BCD error is simple with a Windows installation disk. But if you don’t have one, you can restore Windows Server 2012 to a previous state if you’ve created a system or disk backup. To do this, make a bootable media to start the server. You can also fix the BCD error without a disc by using a professional tool.

Method 2. Run AOMEI Partition Assistant to fix BCD errors

AOMEI Partition Assistant is a powerful disk manager tool that can fix many issues. Its Boot Repair feature is useful for fixing common issues like system boot failures with errors such as "Boot Configuration Data file is missing" or "Boot Configuration Data file is corrupted." It also helps with boot problems after updates, boot conflicts in multi-OS setups, and boot sector corruption from viruses or other issues on Windows Server 2025, 2022, 2019, 2016, 2012 (R2).

Case 1: Repair a running PC

Step 1. Install and launch AOMEI Partition Assistant. In the Main Tab, please click the "Recover" tab and select "Boot Repair".

Step 2. The Boot Repair tool will pop up. Please click "Next" to start the system’s boot entries scan process.

Step 3. After the process is completed, it will display the scan result: system paths, system versions, and boot status. And, all repairable boot entries will be available to select.

Advanced Settings: Select a location to store the repaired boot entry.

Repair to the current disk: The system will boot from the current disk and ensure the boot files are complete and functioning properly. (By default)

Repair to another disk: This operation will repair the boot entry or create a new system boot entry to ensure the system can boot from the disk you select.

Step 4. Select one/multiple repairable boot entries you want to repair and click the "Repair" button to start the boot repair.

Step 5. Wait for the repair process to finish. Once it is finished, you can check the repair result. If it succeeds, you will get a "Repair Successfully" result.

Case 2: Repair Boot for PC that is unable to Boot

If your computer cannot boot, please create a Windows Server 2019 bootable USB first.

Step 1. Prepare a blank USB and connect it to a working PC that has installed AOMEI Partition Assistant, click "Recover" >"Boot Repair" and then click the "create a bootable disk" option to create a WinPE "Boot Repair" disk.

Step 2. Boot the PC that cannot boot into WinPE. It will automatically load the Boot Repair tool and start the boot entries scan process. All boot entries will be displayed.

Step 3. Select the repairable boot entries you want to repair and click the "Repair" button to start the repair.

Step 4. Once the repair is repaired successfully, you can remove the bootable disk and boot the PC from the original system drive.

Method 3. Rebuild corrupted MBR

If the BCD error has been caused by damaged or corrupted MBR, AOMEI Partition Assistant also offers the option like Rebuild MBR for repairing boot.ini for Windows Server 2012.

Step 1. Connect a USB drive to the healthy PC. Install and launch AOMEI Partition Assistant on that PC as well. At the main interface, click on Make Bootable Media in the “Tools” in the top toolbar, and follow the steps to complete creating. Burn to CD/DVD and Export ISO File are available, too. You can also add certain drivers for the Server 2012 before creating.

Step 2. Insert the bootable media to the Server 2012 and boot off the machine. If it falls back to the local disk, you need to change the boot priority to the bootable media in BIOS.

Step 3. Once you login AOMEI Partition Assistant Server will start automatically. Right-click the disk you want to fix (usually the system disk in this case) and select Rebuild MBR.

Step 4. In the popping up window, select the type of MBR for Windows Server 2012, i.e. Windows 7/8/10/2011/2012 option, and click OK.

Step 5. Click Apply and then Proceed to execute the pending operations. Then, restart your Server for repair.

Conclusion

To repair boot.ini for Windows Server 2012(R2), you can run CMD or a handy tool like AOMEI Partition Assistant. With our guide, you could easily and effectively fix issues when your Windows Server 2012(R2) failed to boot. This multifunctional software also helps to recover lost files from Windows Server, manage partitions, extend drive space, convert MBR to GPT in Windows Server 2012 R2, and so on.