How to Configure Microsoft ADFS with Azure MFA as Primary Authentication

In order to setup Azure MFA as Primary Authentication with AD FS, this does require you to move to Azure MFA (cloud-based version). I have not deployed Azure Multi-Factor Authentication Server (on-prem/hybrid version) in a few years for anyone as pretty much everyone I work with has moved on to cloud-based Azure MFA. Feature parity is pretty close to the same at this point and in my opinion, the days of Azure MFA Server on-prem are numbered. If you’re still on the on-prem Azure MFA Server, it is very easy to migrate to the cloud-based Azure MFA. I have moved several companies over the last few years and if anyone needs a guide just let me know and I can write one.

I’m going to assume you have a working AD FS environment already that is federated with Azure AD using Azure AD Connect.

How to configure AD FS and Azure MFA to work like this

1. Log into your AD FS server. In my example, I am using AD FS 4.0 with a Farm Behavior Level (FBL) set to 3 which means Windows Server 2016 and an Active Directory 2016 schema. You can always run the PowerShell cmdlet “Get-AdfsFarmInformation” on your AD FS server to show your FBL version. Go ahead and open the AD FS console:

2. Click AD FS > Service > Authentication Methods > Edit Primary Authentication Methods

3. You’ll notice for primary authentication there is currently no option for Azure MFA. There will be a notice asking you to integrate with an Azure AD tenant in order to use Azure MFA. Again, remember this is not the Azure MFA Server from on-prem which is usually configured on the Multi-factor tab. This is the cloud-based Azure MFA which means AD FS needs to talk directly to your Azure tenant and Azure AD to invoke Azure MFA:

4. Log into your Azure tenant using Login-AzAccount PwerShell and copy out your Tenant ID.

5. On your AD FS server, open up an Administrator PowerShell window and type the below command to generate a tenant certificate to use with Azure MFA: $certbase64 = New-AdfsAzureMfaTenantCertificate -TenantID

$certbase64 = New-AdfsAzureMfaTenantCertificate -TenantID

6. This cert needs to be generated in each AD FS server in your farm. You can open up the Certificates console and see it is stored under Local Computer > Personal > Certificates as a Client Authentication certificate. Note that the default expiration date is 2 years from the date you generate it so be mindful that you need to renew this and include it in your AD FS certificate maintenance plans.

7. Now you need to enable the AD FS servers to communicate with the Azure Multi-Factor Auth Client already registered in your Azure AD. The cert you just generated will be used as credentials to the Service Principal for the Azure Multi-Factor Auth Client. In your Administrator PowerShell window, type: Install-Module -Name AzureAD

Install-Module -Name AzureAD

and accept all the prompts to get the Azure AD module installed from the PSGallery.

8. Then type: Install-Module MSOnline

Install-Module MSOnline

and accept the prompt to get the Microsoft Online Services module installed.

9. Now type: Connect-MsolService


and a web view will open up asking you to sign-in to Azure. I typically use a global admin account here:

10. Once authenticated, we need to set the Service Principal to use the new cert with Azure MFA. Type in: New-MsolServicePrincipalCredential -AppPrincipalId 981f26a1-7f43-403b-a875-f8b09b8cd720 -Type asymmetric -Usage verify -Value $certBase64

New-MsolServicePrincipalCredential -AppPrincipalId 981f26a1-7f43-403b-a875-f8b09b8cd720 -Type asymmetric -Usage verify -Value $certBase64

The App Principal ID in this step of “981f26a1-7f43-403b-a875-f8b09b8cd720” is for the Azure Multi-Factor Auth Client is not something unique you need to change. Leave it as-is and don’t modify this GUID. Type the line exactly as I have it above. Make sure to do it on all your AD FS servers.

11. Now the next step is where we tell AD FS to use your Azure AD tenant with Azure MFA. You only need to run this from one of your AD FS servers since all servers will see this config change: Set-AdfsAzureMfaTenant -TenantId <YourTenantID> -ClientId 981f26a1-7f43-403b-a875-f8b09b8cd720

Set-AdfsAzureMfaTenant -TenantId <YourTenantID> -ClientId 981f26a1-7f43-403b-a875-f8b09b8cd720

12. Now go into Services on each of your AD FS servers and restart the “Active Directory Federation Services” service.

13. Close any AD FS MMC consoles you have open and then re-open and go to Edit Authentication Methods again. Now you will see a new Primary authentication option of Azure MFA for use with both your Extranet and Intranet!

14. Go ahead and check the box next to them so you can choose when the Azure MFA option is shown to users. Most companies I work with choose to only enable it for their Extranet, meaning users that come in through the AD FS WAP (Web Application Proxy) servers in the DMZ. I’m just going to select both in this example since I will be testing logins from an internal Windows 10 desktop in the next few steps and I want to see the Azure MFA option show up:

The AD FS with Azure MFA as Primary Authentication user experience

15. Now on my Windows 10 desktop, I am going to navigate to the IdP initiated AD FS login URL to test this. You’ll also probably want to disable Windows Authentication (IWA aka Integrated Windows Authentication) on the Intranet in AD FS if this a test environment just so you don’t get auto-logged in. Go to:

Hit the “Sign in to this site” radio button and then click Sign in.

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