Skip to content
How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights

How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights

Written By Anoop C Nair
Last Updated March 3, 2025
Posted In Entra
SHARE

Let’s discuss how to Use Microsoft Intune Connector with Multiple Domains Security Update Insights. Microsoft introduced an important security change as part of a secure future initiative called Intune Connector for Active Directory. The change has many impacts.

The new enhancement will impact customers deploying Microsoft Entra hybrid joined devices with Windows Autopilot and provide guidance on how to prepare. With the new update, Windows Autopilot uses the Intune Connector for Active Directory to deploy devices that are Microsoft Entra hybrid joined.

Do you know what the Intune Connector for Active Directory is? It is a tool used in conjunction with Windows Autopilot to deploy devices that are Microsoft Entra hybrid joined. The Intune Connector for Active Directory, also known as the Offline Domain Join (ODJ) Connector.

Microsoft updated the Intune Connector for Active Directory to strengthen security in customers’ environments. In this update, a Managed Service Account (MSA) is used instead of a SYSTEM account. In this blog post, I will explain more about the Intune Connector for Active Directory.

Patch My PC
How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights - Fig.1
How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights – Fig.1

How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights

Due to this new update, the old connector, which uses the local SYSTEM account, will no longer be available for download in Intune and will stop being supported in late May 2025. After that, Microsoft will stop accepting enrollments from the old connector build. Existing customers who already have the old Connector for Active Directory can continue to work.

Managed Service Account (MSA)

A Managed Service Account (MSA) is a type of domain account in Active Directory designed to provide automatic password management and simplified Service Principal Name (SPN) management. An MSA can run services on a computer in a secure and easy to maintain manner, while maintaining the capability to connect to network resources as a specific user principal.

Types of MSADetails
Standalone Managed ServiceIt is used on a single domain-joined machine and can only access resources within that domain
Group Managed ServiceThese provide the same functionality as sMSAs but extend that functionality over multiple servers.
How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights – Table.1
How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights - Fig.2
How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights – Fig.2

Account Permissions Required between the New and Old Connector

There are many differences between new and old connectors. Each connector has many account permissions required. The table below shows the account permissions required for each connector.

FeaturesOld ConnectorNew Connector
Logged on accountSYSTEMDomain\MSA
Password managementSet by user, subject to domain rules
Privilege set size (see notes for more details)MAX
Registry access rightsFull, implicit
Enrollment certificate rightsFull, implicit
Create computer object rights (required for hybrid Autopilot scenario)If connector is on the same machine as domain controller, unlimited.

If connector is not on the domain controller, delegation required
How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights – Table.2

Setting Up the Connector

To set up the Intune Connector for Active Directory, there are several steps you must follow before beginning. First, you need to uninstall the existing connector by uninstalling it from the Settings app on Windows. Then, uninstall it using the ODJConnectorBootstrapper.exe (select Uninstall). The following table shows the minimum requirements needed to install and set up the new connector.

RequirementsDetails
Downloading the connector build from IntuneMicrosoft Entra account with Intune Service Administrator permissions
Installation.Net 4.7.2
Windows Server with 2008 R2 functional level
Setting up the connectorLocal administrator permissions
Microsoft Entra account with an Intune license assigned and Intune Service Administrator permission
Domain account with local administrator privileges
Domain account should have permission to create msDS-ManagedServiceAccount objects
How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights – Table.3

Downloading the Connector

From the Intune admin center, you can download the new connector and install it in your environment. After that, go to the connector wizard, choose Sign In, and sign in with a Microsoft Entra account with Intune service admin permissions. You’ll notice a new Configure Managed Service Account option.

After signing in, the connector will enroll, and only the Configure Managed Service Account option will be available. The account with Intune admin permissions should select that option to complete the set-up.

How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights - Fig.3
How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights – Fig.3

Configuring Organizational Units (OUs) for Domain Join

To create computer objects in any OU, MSAs don’t have access by default. You will need to update the ODJConnectorEnrollmentWiazard.exe.config file, you wish to use a custom OU for the domain join. This can be done at any time (either before enrollment, or after the connector is enrolled).

  • Update ODJConnectorEnrollmentWizard.exe.config:
  • Default location is “C:\Program Files\Microsoft Intune\ODJConnector\ODJConnectorEnrollmentWizard”
  • Add all the OUs required in OrganizationalUnitsUsedForOfflineDomainJoin
  • OU name should be the distinguished name (see Additional information section)

Note: MSA is only granted access to the OUs configured in this file (and the default Computers container). If any OUs are removed from this list, completing the rest of the steps will revoke access

How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights - Fig.4 - Creds to MS
How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights – Fig.4 – Creds to MS

After that Open ODJConnectorEnrollmentWizard (or restart it if it was open) and select the “Configure Managed Service Account” button. Follow the below screenshot.

How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights - Fig.5 - Creds to MS
How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights – Fig.5 – Creds to MS

Then, you will get a pop-up window that shows a success message, such as “A Managed Service Account with name “msaODJdSpXW” was successfully set up. Click on the OK button.

How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights - Fig.6 - Creds to MS
How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights – Fig.6 – Creds to MS

How to Use Intune Connector with Multiple Domains

Customers who are already using the connector with more than one domain will be able to use the new connector by setting up a separate server per domain and installing a separate connector build for each domain.

Configuring the Connector

To configure the connector you have to follow some steps. The Intune Connector for Active Directory needs to be installed on each domain that you plan to use for domain join. If you need to have a second account redundancy, you will need to install the connector on a different server (in the same domain).

To ensure the connector is configured correctly, and that the MSA has appropriate permissions on the desired OUs, follow the above steps. To ensure that all connectors are present in the in the Microsoft Intune admin center. Follow the below steps and screenshot.

  • Open Microsoft Intune admin center
  • Go to Devices > Enrollment > Windows
  • Under Windows Autopilot, select Intune Connector for Active Directory)
How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights - Fig.7
How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights – Fig.7

After that, you can see the available versions of Connect on your tenant. To configure the connector, you need a version greater than 6.2501.2000.5. Look at the screenshot below.

How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights - Fig.8 - Creds to MS
How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights – Fig.8 – Creds to MS

Configure Domain Join Profile

To configure a domain join profile, follow these steps: Create a domain join profile for each domain that you want to use for hybrid joining devices during Autopilot. Target the domain join profile to the appropriate device groups. Domain join profiles are configured to target different groups with different domain names.

Example 1

On the below screenshot, the selected group is [zatoyer]f11 domain join. On the The expected result for this is Connector in domain F11.F1.com will only join domain F11.F1.com. The following are the configuration settings details.

  • Computer name prefix – ODJF11-
  • Domain name – F11.F1.com
  • Organizational unit – OU=Autopilot,OU=HybridDevices,DC=F11,DC=F1,DC=com
How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights - Fig.9 - Creds to MS
How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights – Fig.9 – Creds to MS

Example 2

The screenshot below shows the second example. The[zatoyer] f12 domain join is the domin name. The expected result is that the Connector in domain F12.F1.com will only join domain F12.F1.com. The following are the configuration settings details of the domain join.

  • Computer name prefix – ODJf12
  • Domain name – F12.F1.com
How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights - Fig.10 - Creds to MS
How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights – Fig.10 – Creds to MS

Retrieving Organizational Unit Distinguished Name

To customize the OUs that the MSA has access to, here are two easy methods to retrieve their distinguished names. The following is the structure.

How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights - Fig.11 - Creds to MS
How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights – Fig.11 – Creds to MS

PowerShell Script

The following are the PowerShell scripts for customizing the OUs that the MSA has access to. You can copy the script below and use it to customize the OUs that the MSA has access to.

How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights - Fig.12 - Creds to MS
How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights – Fig.12 – Creds to MS

Active Directory Users and Computers

To Active Directory Users and Computers, Select “View” from the menu, and enable “Advanced Features”. Then, right-click on the specific OU and click “Properties”. Navigate to the “Attribute Editor” tab
Select “distinguishedName” attribute and click “View”.

How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights - Fig.13 - Creds to MS
How to Use Microsoft Intune Connector with Multiple Domains Security Update Insights – Fig.13 – Creds to MS

Need Further Assistance or Have Technical Questions?

Join the LinkedIn Page and Telegram group to get the latest step-by-step guides and news updates. Join our Meetup Page to participate in User group meetings. Also, Join the WhatsApp Community to get the latest news on Microsoft Technologies. We are there on Reddit as well.

Resource

Microsoft Intune Connector for Active Directory security update

Author

Anoop C Nair has been Microsoft MVP from 2015 onwards for 10 consecutive years! He is a Workplace Solution Architect with more than 22+ years of experience in Workplace technologies. He is also a Blogger, Speaker, and Local User Group Community leader. His primary focus is on Device Management technologies like SCCM and Intune. He writes about technologies like Intune, SCCM, Windows, Cloud PC, Windows, Entra, Microsoft Security, Career, etc.

Written by

Anoop C Nair is Workplace Technology solution architect with 25+ years of experience in global enterprise organizations such as JP Morgan, Capgemini, etc. Microsoft Certified Trainer. Microsoft MVP from 2015 onwards for consecutive 11+ years! He also conducts Intune and modern workplace tech training for enterprise organizations. He is Blogger, Speaker, and Founder of HTMD Community and HTMD Conference. His main focus is on Device Management technologies like Intune, Windows, Cloud PC. He writes about technologies like Intune, SCCM, Windows, Cloud PC, Windows, Entra, Microsoft Security.

Discussion

Join the discussion

Your email address will not be published. Required fields are marked *

Related guides

Entra

Entra ID SSPR Improves Security with Registered Authentication Methods | Impact on Unregistered Users Starting September 2026

Key Takeaway Entra ID SSPR Improves Security with Registered Authentication Methods! Starting September 7, 2026, Microsoft Entra ID Self-Service Password Reset (SSPR) will require users to verify their identity using explicitly registered authentication methods. Directory-sourced contact information, such as mobile phone numbers, business phone numbers, and alternate email addresses, will no longer be accepted for […]

AC Anoop C Nair 4 min read
Entra

Explicit Forward Proxy in Microsoft Entra Internet Access Helps Secure VDI BYOD and Clientless Browsing

Key Takeaways Explicit Forward Proxy in Microsoft Entra Internet Access! This feature allows organizations to use secure web and AI gateway capabilities without deploying the Global Secure Access client, making it useful for browser-based and lightly managed environments. It works with browsers that support Proxy Auto-Configuration (PAC) files. Since this is a prerelease feature, Microsoft […]

AC Anoop C Nair 3 min read
Cloud

Microsoft Enables Entra Writeback for Cloud-Managed Remote Mailboxes to Help Remove Last Exchange Server

Key Takeaways: Let’s discuss about Microsoft Unlocks Entra Writeback for Cloud-Managed Remote Mailboxes to Help Remove Last Exchange Server. For customers with no remaining dependency on their last Exchange Server, a guide for decommissioning your last Exchange Server. Microsoft announced the Public Preview of Cloud-Managed Remote Mailboxes. Microsoft is excited to share these two new milestones […]

AC Anoop C Nair 3 min read