How to Set Mobile Device Management Authority

In Windows Intune you can choose to set the Mobile Device Management Authority for Mobile Device Management. The Mobile Device Management Authority can be set to Windows Intune OR System Center Configuration Manager (SCCM/ConfigMgr). Consider carefully whether you want to manage mobile devices by using Windows Intune only or SCCM with Windows Intune Integration. After you set the mobile device management authority to either of these options, this cannot be changed.

In Windows Intune you can set the Mobile Device Management Authority from within the Admin Console. More information about this choice can be found on Microsoft TechNet.

1.Open the Windows Intune administrator console.
2.In the workspace shortcuts pane, click the Administration icon.
3.In the navigation pane, click Mobile Device Management Setup.
4.In the Tasks list on the Policy Overview page, click Set Mobile Device Management Authority.
5.The Set Mobile Device Management Authority dialog box appears, and it prompts you to choose whether to use Windows Intune to manage the mobile devices in your account. Do one of the following: Click Yes to use Windows Intune to manage mobile devices for your account. If you set Windows Intune as the management authority, you must manage mobile devices by using the Windows Intune administrator console.
Important: If you plan to use SCCM to manage mobile devices for your account, do not set the mobile device management authority to Windows Intune. To set the mobile device management authority to SCCM, you must use your organizational account to create a Windows Intune subscription from within the SCCM console, and select the option to allow Configuration Manager to manage the subscription.

In SCCM you can set the Mobile Device Management Authority from within the Administration pane. More information about this can be found on Microsoft TechNet.

1.In the Configuration Manager console, click Administration.
2.For System Center 2012 Configuration Manager SP1: In the Administration workspace, expand Hierarchy Configuration, and click Windows Intune Subscriptions.
For System Center 2012 R2 Configuration Manager: In the Administration workspace, expand Cloud Services, and click Windows Intune Subscriptions.
3.For System Center 2012 Configuration Manager SP1: On the Home tab, in the Create group, click Create Windows Intune Subscription.
System Center 2012 R2 Configuration Manager: On the Home tab, click Add Windows Intune Subscription.
4.On the Introduction page of the Create Windows Intune Subscription Wizard, review the text and click Next.
5.On the Subscription page, click Sign in and sign in by using your Windows Intune organizational account. Select the Allow the Configuration Manager console to manage this subscription check box. When you select this setting, you will only be able to manage mobile devices by using the Configuration Manager console. To continue with your subscription, you must select this option.
Important: Once you select Configuration Manager as your management authority, you cannot change the management authority to Windows Intune in the future.

In case of bad decision it's possible to contact Microsoft Support on this to reset the Mobile Device Management Authority for your account. In that case all managed computers and/or mobile devices must be removed from Windows Intune. After the reset it's possible to set the Mobile Device Management Authority again.