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Mobile Device Management with Configuration Manager 2012 R2 - Part 1. Integrating Microsoft Intune

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Mobile device management (MDM) in Configuration Manager is possible via the following methods

  • Enrollment by Configuration Manager
  • Mobile Device Legacy Client
  • Exchange Server Connector

The methods above provide you with different abilities, Enrollment by Configuration Manager let’s you manage older and less popular hardware such as

  • Windows Mobile 6.1
  • Windows Mobile 6.5
  • Nokia Symbian Belle

whereas the Mobile Device Legacy client can manage similar older mobile operating systems such as

  • Windows CE
  • Windows Mobile 6.0

Finally you can do remote wipe or settings control for devices managed by Exchange 2010 using Exchange ActiveSync by using the Exchange Server Connector.


How does Microsoft Intune fit into all of this ?


Microsoft Intune can be utilized in two main ways

  • Standalone - Intune managed and run in the cloud
  • Hybrid - An on-premise System Center 2012 R2 Configuration Manager environment which is connected to Microsoft Intune in the cloud

As you’ll probably want a single pane of glass for managing your modern mobile devices as well as your company servers and computers, integrating Microsoft Intune with Configuration Manager 2012 R2 is a logical next step. In this post I’ll show you how to integrate Microsoft Intune with System Center 2012 R2 Configuration Manager to form a hybrid scenario in order to perform unified Mobile Device Management.


By integrating System Center 2012 R2 Configuration Manager with Microsoft Intune you have unified Mobile Device Management (MDM) of modern mobile devices such as Android, Windows Phone 8, iOS, Windows RT. This ability has been in place since Configuration Manager 2012 SP1 but has been updated with several new abilities and refined with the release of System Center 2012 R2 Configuration Manager and several times since then, in addition, Windows Intune was renamed to Microsoft Intune (see this blog post for details).


When you use Configuration Manager with Microsoft Intune, you have the following management capabilities:

  • You can retire and wipe devices.
  • You can configure compliance settings on devices. These include settings for passwords, security, roaming, encryption, and wireless communication.
  • You can deploy line of business apps to devices.
  • You can deploy apps from the store that the device connects to, Windows Store, Windows Phone Store, App Store, or Google Play.
  • You can collect hardware inventory.
  • You can collect software inventory by using built-in reports.

In this mini-series of guides on managing modern devices I will show you what you need to do to successfully integrate Configuration Manager 2012 R2 with Microsoft Intune and then manage them.


Step 1. Get a Microsoft Intune account

If you don’t already have a Microsoft Intune account then head over to the Enterprise Mobility Suite page and you should see a heading which says "Try the Microsoft Enterprise Mobility Suite" and beneath that is a Try Now button.


Click on the Try Now button to test a 30 day free trial. After the 30 day free trial is complete you'll be asked if you want to buy a subscription as Microsoft Intune isn’t free, there is licensing cost involved. To get details of those costs please review the Microsoft Intune Licensing FAQ which can be found here.


try microsoft intune free for 30 days.png


After signing up you can login to the Microsoft Intune Account portal using the credentials you specified (while will be something like user@domain.onmicrosoft.com) as shown below


login with your onmicrosoft com account.png


You will be presented with a webpage page like the one below:


account portal.png


At the top of the screen you’ll notice three main tabs,


Company Portal - Admin Console - Account Portal.png


These tabs are described below and each one is click-able and will take you to the respective page once you have created credentials above:

The Company Portal pictured below, will open a new window that shows applications added to Microsoft Intune and deployed to the logged in user, it will show All devices (for the logged on user, with a maximum of 5 devices per user) and some support options.


Company Portal.png


The Admin Console pictured below, is where you’ll do your day to day activities in Microsoft Intune for Standalone Intune environments. This is Silverlight powered so you’ll most likely get prompted to install Silverlight if it’s not already installed.




The Account Portal pictured below, is where you manage Microsoft Intune subscriptions, licenses and initial setup of Intune Users.


account portal.png


Step 2. Add a public company domain

In order to ensure users are synchronized correctly you must create or have access to a verified public domain within the Microsoft Intune Account Portal. If this step is not performed you might end up with users with onmicrosoft.com UPN (User Principal Name) related names.


Logon to https://account.manage.microsoft.com/ which is the Microsoft Intune Account Portal and click on Domains under Management in the left pane.


domains under management.png


Next, click on Add a Domain and enter your domain name as shown in the screenshot below:


specify a domain name.png


Click on Next, you’ll be asked if you want to verify using a TXT or MX record, I have chosen TXT in this example (and it’s the recommended choice as the other option could potentially give you issues).


To allow Microsoft Online Services to verify your domain you will need to logon to your domain registrar or DNS provider for the domain in a separate web browsing session. The steps are listed below

  • Logon to your Domain provider (eg: GoDaddy) and select the domain that you're verifying, editing or adding a DNS record to.
  • In the DNS management area for your account, select the option to add a TXT record for your domain.
  • In the Host or Host name box for the domain, type or paste @. (If your domain registrar doesn’t let you enter an @ symbol then simply remove it (leave the @ blank). An @ in the Hostname represents the blank record for the root domain (eg: windowsintunenoob.com).
  • In the value (or data) box, type or paste MS=ms57610744. (Note: this was the value I was prompted to add, your value will most likely be DIFFERENT, enter the value that you were given.) Depending on the website, this box may be labeled Text, Value, Address, Points to, or TXT record.
  • Save your changes.

Once done you can check those settings by clicking on Edit again and it should look something like this (again, this is in your DNS providers web page, not the Intune Account Portal).


windowsintunenoob dns record editing.png


In the Microsoft Intune account portal Domain section, click on Verify to verify the Account like in the screenshot below


verify account.png


Once the account is verified you should see something like the following


verified domain name.png


Click on close


Step 3. Create a CNAME DNS entry

In order to enroll Windows Phone 8, Windows RT and Windows 8.1 devices you’ll need to create a CNAME DNS entry which directs EnterpriseEnrollment to manage.microsoft.com


In your domain registrar, add a new CNAME record like the one below (note: the screenshot below shows a different domain name to my Intune domain name, use whichever is appropriate for your company)


enterpriseenrollment cname dns.png


To do this create a CNAME resource record for the verified domain in the public DNS. The CNAME resource record must contain the following information:

  • Alias name: EnterpriseEnrollment
  • Fully qualified domain name (FQDN) for the target DNS host: EnterpriseEnrollment.manage.microsoft.com


Step 4. Setup User Principal Names for your Users

Before you synchronize the Active Directory user account, you must verify that user accounts have a public domain UPN. For more information, see Add User Principal Name Suffixes in the Active Directory documentation library.


To ensure that users that will be managed have the above Public Domain as their primary User Principal Name (UPN) in Active Directory you can verify the UPN attribute in Active Directory Users and computers. The Active Directory attribute for each user is synced up for each user to the corresponding user in Microsoft Intune. You can apply the UPN suffix via a script or manually in ADSIedit. To create a UPN suffix for a forest see this post (thanks @NickolajA).


apply UPN to user names.png


Step 5. deploy and configure Active Directory Federated Services (ADFS)

If you plan to use single sign-on, Deploy and configure Active Directory Federated Services (ADFS) as described here.

In this guide I am not configuring or using ADFS for SSO but you may want to do so. If I do publish a guide for setting up ADFS in the future i'll amend this post to reflect that.


Step 6. Enable Active Directory synchronization


Note: The dirsync tool is being depreciated, use the AD Connect tool instead from here. For a comparison chart between the tools – DirSync, AADSync, AD Connect, and FIM, refer to this link:




Activating Active Directory synchronization allows you to automatically copy users, security groups and other objects from your local (on premise) Active Directory to (a cloud based) Windows Intune. In the Windows Intune Admin Console select Users and click on Active Directory synchronization: Set up.


Dirsync Setup.png


Follow the guidance on the page it links to (which are the first 3 steps shown below) and when ready click on Activate




Another window will pop up, click on Activate again.


Activate active directory synchronization.png


If all goes well you’ll be informed that Active Directory synchronization is activated.


Active Directory synchronization is activated.png


Next you download the actual dirsync.exe tool to run on your Domain Controller, choose the correct architecture.


download the dirsync tool.png


Once downloaded make sure that you have .NET Framework 3.5 SP1 and .NET Framework 4 installed on the computer which you run the DirSync tool, then run the tool with suitable credentials. (I ran it as a Domain Enterprise Administrator).


run dirsync.png


Click next at the welcome


welcome to dirsync.png


Accept the EULA and then select the installation directory


installation folder for dirsync.png


And click next again to let it install


installing DirSync.png


When the installation is complete (it takes some time to install all the components) click Next and place a checkmark in Start Configuration Wizard now then click Finish.


dirsync start the configuration wizard now.png


On the DirSync tool Configuration wizard welcome screen click Next and logon with your Admin credentials that you used when setting up Microsoft Intune. For example in my lab I use


These credentials will be saved and used to synchronize changes to your users from your organization’s on-premise Active Directory with Windows Azure Active Directory.


setup dirsync with intune account.png


Next enter your active directory enterprise administrator credentials, after entering your AD credentials (eg: windowsintunenoob\EntAdmin)


login with local credentials.png


If you want to enable Hybrid Deployment select it here


Hybrid deployment.png


next you'll be prompted if you want to enable Password Synchronisation. If you require this then select Enable Password Sync, and click Next, this is not the same as Single Sign on, but does reduce complexity as described here.


Password Sync.png


Once done you’ll see configuration complete


dirsync confguration complete.png


Let it complete until Finished. Once done if will allow you to Sychronize your directories


synchronize your directories now.png


You’ll then get a message prompting you to click on a link for details about the Active Directory synchronization progress - http://technet.microsoft.com/en-us/library/jj151797.aspx


Click Ok.


see verify directory sycnchronization.png


At this point you can wait a bit before once again browsing the Users link in Microsoft Intune. It should have populated with your users if all went well with DirSync. In addition you can browse Groups and you’ll see your Active Directory User Groups listed.


Users synched from lab.png


Tip: You can force a DirSync manually by double-clicking DirSyncConfigShell.psc1 in the Windows Azure Active Directory Sync installation directory, to open a Windows PowerShell window with the cmdlets loaded. In the Windows PowerShell window, type Start-OnlineCoexistenceSync, and then press ENTER.


start online co existence.png


And finally, you can also monitor DirSync activity using the MiiSync tool located in C:\Program Files\Windows Azure Active Directory Sync\SyncBus\UIShell, however you should log off as the current user and logon again before running the tool (so that the correct AD Security group membership is updated for your profile.)




Note: If you haven't verified your own domain name with Microsoft Intune as the primary domain, then the Primary UPN of your user accounts in Active Directory that are added as members of the Windows Intune Users (or Microsoft Intune Users) collection must match the domain you are using in intune, for example : someuser@somedomain.onmicrosoft.com. Also keep in mind that user accounts must be activated if you are not synchronising passwords using DirSync - which means before that user can enroll a device they should login to the Intune Portal themselves on a web browser and set/change their password.



Step 7. Perform Active Directory User Discovery

In the Configuration Manager console perform a User discovery as shown below, this will mean Configuration Manager will have the most up to date details of your users including any UPN changes you made above.


Run Full Discovery now.png


Step 8. Create a user collection called Microsoft Intune Users

Micrososft Intune will need a user collection to allow users to enroll their devices, so let’s go ahead and create one. In the System Center 2012 R2 Configuration Manager console select Assets and Compliance then select User collections, right click and choose Create User Collection.




The create user collection wizard will appear, give the collection a suitable name like Microsoft Intune Users and limit it to the All Users collection or whichever User collection you deem appropriate.


Note: Earlier versions of this guide created a collection called Windows Intune Users, however since Microsoft renamed Windows Intune to Microsoft Intune in October 2014, you should probably do the same, therefore any screenshots or references to a Windows Intune Users collection in these guides should be replaced with Microsoft Intune Users.


create microsoft intune users collection.png


Continue through the wizard until completion. Once you’ve created the User collection add some users to it using whatever method you wish (direct membership or query).


Step 9. Add Microsoft Intune Subscription

In the System Center 2012 R2 Configuration Manager console select Administration, and expand Cloud Services, select Microsoft Intune Subscriptions from the options available.


Configuration Manager console.png


In the ribbon above, click on Add Microsoft Intune Subscription


Add Windows Intune Subscription.png


The create Microsoft Intune subscription wizard appears


create windows intune subscription wizard.png


Click on Next and you’ll be presented with the Microsoft Intune sign in page.


windows intune subscription sign in.png


This will pop up a Set the Mobile Device Management Authority window.


Set the Mobile Device Management Authority.png


Place a checkmark in the check box and click on OK. Selecting this choice will ensure that Configuration Manager will manage your mobile devices by using the Microsoft Intune connector and any mobile devices currently managed by Intune will now be managed by Configuration Manager. This is not reversible, so if you want to manage your mobile devices with Windows Intune then don’t select this option.


Tip: If you have computers currently managed by Intune then they will remain managed by Intune. Only mobile devices will be managed by Configuration Manager if you chose it to be the authority above.


You’ll be presented with the login page, fill in your details used in Step 1 and click on Sign In.


sign in to subscription.png


After signing in click on next, you’ll see the General Configuration screen


general configuration.png


Click on browse and browse to the Windows Intune Users collection we created earlier, next fill in the Company name and URL to company privacy documentation, finally select the color scheme for the company portal and the Site code used for Device Management.


general configuration filled in.png


Next you will get the platform support screen, leave all 4 choices deselected. We will enable one of them in the next part of this guide.


The 4 choices you have and their requirements if any are explained below:

  • Android: There are no platform requirements for Android devices.
  • iOS: You will need an Apple Push Notification Service (APNs) certificate.
  • Windows: You will need to specify sideloading keys. Sideloading keys let you install apps that are not in the Windows Store.
  • Windows Phone 8: You must have a code-signing certificate. The certificate will sign the company portal app and all other apps deployed by Configuration Manager.

For now, select no platforms, we will add them later.


select platforms.png


Then click next, and fill in the company contact information


company contact information.png


And add your company logo


company logo.png


And click through to the completion notice, take note of the warning at the top of this screen.


subscription wizard complete - notice the warning.png


Step 10. Add the Microsoft Intune Connector role

Note: The Windows Intune Connector role does not appear until after you have completed the Windows Intune Subscription wizard.


In Site Configuration, expand Servers and Site System roles and note that you now have a new site system server listed, namely manage.microsoft.com.


manage dot microsoft dot com.png


Select your Primary server and right click, choose Add Site System roles.


Note: If you have a hierarchy, you must install this role on the CAS server.


add site system roles.png


Fill in appropriate details for the General page and if you use a Proxy to access the internet then add those details on the Proxy page, on the System role selection page select our Windows Intune Connector role.


add the Windows Intune Connector role.png


The Windows Intune Connector role is like a gateway between Configuration Manager and Windows Intune (in the cloud) and it checks every 5 minutes for changes and relays that information up to manage.microsoft.com.


Complete the Add Site System Roles wizard.


add site role completed.png


To verify if the connector role installs correctly refer to the Sitecomp.log logfile which records details of the Windows Intune connector role installation.


Congratulations you've completed the first part of this mini-series, in the next part we will add iOS support.





Log Files

The following Log Files are useful for troubleshooting problems with Windows Intune Integration in System Center 2012 R2 Configuration Manager.

  • clouddmp.log
  • dmpdownloader.log
  • dpmuploader.log
  • cloudusersync.log

For a full list of logfiles related to the Windows Intune Connector see here


Related reading


You can download a Microsoft Word version of this guide here.


How can I manage modern devices in System Center 2012 R2 Configuration Manager - Part 1 - Integrating Windows Intune.zip

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Thanks Nial for the wonderful guide (as always).


1. I cant find the link to the next part of this series (iOS support), am I missing URL or its under production.


2. For UPN suffix, I configured my AD DS setup with public domain and noticed that correct UPN is already there, no need to configure it separately, am I correct?

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Thanks Nial for reply and providing the URL to next part.


Regarding UPN, when I selected multiple users -> Properties ->Account Tab ->
I can see that UPN suffix shows the correct value but the check box was unselected, I place a tick box , click, apply ... then this UPN suffix check box removed automatically. I don't know if its normal or not. Have you experienced the same when you selected the UPN suffix check box?

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Hi Niall,


great article (already told you that!)!

So if I want to manage my Android device and turn off the camera, I need to do that at manage.microsoft.com under Policies, right?

Is it expected that I only see the enrolled device in my CM12 console and not in Intune? I still deploy the policies to all my "Intune All Users Group", right?

Looks like the policy I configured doesn't get applied to my device...




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thanks David !

I will be covering Android devices shortly, just need time to write the guides... but basically you enable Android support (like we did with iOS support in part 2) and then download and install the SSP from Google Play, once done enroll the device and you'll be able to manage it via Configuration Manager - not Intune, once you set the management authority to Configuration Manager then all management of these devices is done via Configuration Manager, so yes what you are seeing is correct, I assume the collection you are referring to is the Windows Intune Users collection we created above in Configuration Manager and not in Intune...?

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I already enrolled my Android device and it shows up with Client inactive (also Ressource Explorer shows me all details) in CM12, but the Policies I configured in Intune don't get applied. (like, "Disable Camera")

I can also "Deploy" Google Play Apps to my Device and install them from the Google Play Store.


What I'm missing is where to configure those Endpoint Policies (like Password Strenght, Camera use, etc). I understand that I'm not managing my devices in Intune, but in CM12, but where do I manage my mobile policies?


I'm now going to download the Windows Phone SDK in order to test that OS as well (although not having a sideloading key for Windows Phone or the script for R2).

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you manage your mobile settings (policies) in CM12 using Compliance Settings, I will post this shortly when and if i get time, but here's a screenshot to give you an idea.


ci mobile devices.png

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