Upgrade VBR to 12.3.1: Setup detected inconsistent configuration

Veeam Backup & Replication version 12.3.1.1139 was recently released on March 19, 2025. This introduces some critical security patches, new features, and performance enhancements. This update strengthens system security and improves reliability, making it essential for all users to upgrade promptly. Therefore, in this guide, I will show you how to upgrade VBR to 12.3.1: Setup detected inconsistent configuration. Please, see How to Create a User and Custom Domain in Entra ID, and How to update Veeam Backup and Replication [VBR].

One of the most critical fixes addressed is CVE-2025-23120. A vulnerability with a CVSS score of 9.9 that allows authenticated domain users to execute remote code. This flaw poses a severe risk to domain-joined backup server. Organizations using domain-joined configurations should apply this update immediately to mitigate potential threats.

Also, see how to Upgrade Veeam Backup and Replication to version 12.2, how to upgrade Veeam Backup and Replication 12.3, and how to perform In-place upgrade of Windows Server 2022 to 2025.

Part A: Download ISO

Upgrade Veeam Backup and Replication from 12.3.0.310 to 12.3.1. You can download the latest version of VBR from this link.

This updater ISO can only be used to update from 12.3.0.310, if that build is not installed the installer will display the message: This update is not compatible with installed product version.

Since, I am already on this version, I will download the ISO from the following page as shown below. If you are not on this version already, I will also show you how to upgrade to the latest version of VBR using the Veeam Recovery Orchestrator 7.2.

Please, see Export and Convert Private Keys to .PEM Format in Windows, how to Fix Trellix ePO DAT and Engine Packages missing, and How to deploy and integrate VHR with VBR.

Mount the Updater ISO

Upon download, please mount the Veeam Backup & Replication 12.3.1 updater ISO. Alternatively, navigate to the VM settings, select the SCSI controller, and attach the installation image.

Double click on the drive as shown below

Alternatively, you could right-click on mount it as shown below.

Now, ensure no jobs are running and proceed to stop the Veeam Backup Service as shown below.

Now, double click on the mounted ISO and click on setup.

Next, you will be prompted with the window below, click on “Install”.

Next, click on Upgrade Veeam Backup and Replication.

Upon initializing the setup, please accept the license agreement.

It recognizes my installed license. You could browse to one as you wish etc., and click on next to proceed.

The wizard will perform system configuration check and prompt you afterwards to specify the service account password.

Next, the system configuration check will be performed.

Below are the components to restore. Do not forget to select “update remote components automatically”. Else, you will be prompted to do this after the upgrade.

As you can see, the upgrade process has started.

For a complete list of all steps performed. Please, take a look at the referenced link on VBR upgrade to 12.3.0

As you can see below, we have successfully upgraded our VBR to the latest version.

Please, proceed and have your services started.

As you can see below, we are running the Build 12.3.1.1139. Congratulation on your upgrade.

Part B: Using the Veeam Recovery Orchestrator 7.2 to Upgrade VBR

You can also upgrade Veeam Backup and Replication from 12.3.0.310 to 12.3.1 by downloading the latest version version of VBR from this link.

Note: When using this ISO, you might run into the following error “Setup has detected inconsistent configuration: some Veeam Backup & Replication components are missing. Remove the installed Veeam Backup & Replication components manually and start the setup wizard again”.

Reason for this error

The package indicated in the SuiteEngine log is missing and must be installed manually before the update to Veeam Backup & Replication 12.3.1 can proceed

Here is how to Fix missing path and delete a Veeam Backup Repository, and ho to Fix Error 1069: Windows could not start the Veeam backup service on local computer.

Resolution

The missing package could be something other than the Microsoft Entra ID Plug-in for Veeam Backup & Replication. However, the vast majority of support cases related to the 12.3.1 update process so far have involved the Microsoft Entra ID Plug-in for Veeam Backup & Replication. In these cases, the package was either manually uninstalled or, in the case of Veeam Recovery Orchestrator, not included during the previous installation.

Once the virtual drive appears, take note of the drive letter

To install the Microsoft Entra ID Plug-in for Veeam Backup & Replication from the updater ISO. Please follow these steps below.

Paste in the following command and update the drive letter to match the mounted Updater ISO.

msiexec /i "D:\Plugins\Microsoft Entra ID\VeeamEntraIdPlugin.msi"

Note: You could Hold [Ctrl]+[Shift] and tap [Enter]. This key sequence will force the Run prompt to execute the command with elevated permissions.

Click Yes on the UAC prompt. Proceed through the Microsoft Entra ID Plug-in for Veeam Backup & Replication installer wizard.

Once the Plug-in is installed, run the Setup.exe from the Veeam Backup & Replication 12.3.1 updater ISO.

I hope you found this article on how to “Upgrade VBR to 12.3.1: Setup detected inconsistent configuration”. Please feel free to leave a comment below.