Managing SharePoint Online via PowerShell has been an integral part of administrative routines for years. But until now, authentication has been heavily tied to user accounts, which has caused problems in environments with multi-factor authentication (MFA) enabled or strict security policies. With the introduction of App-Only Authentication, i.e. certificate-based login for the SharePoint Online PowerShell module, Microsoft is closing a crucial gap: Secure, unattended automation is finally possible without having to rely on user logins.
The goal is clear: Away from interactive logins and towards an architecture that combines automation and compliance. Below, I’ll show you how this method works, why it’s more secure, and how to integrate it into your existing infrastructure.
Background and motivation
The previous authentication via user accounts is problematic for scripts. Once MFA is enforced, classic automations fail because human intervention is required. This is exactly where App-Only Authentication comes in: It uses a registered application in Azure AD that is secured with an X.509 certificate. This eliminates the need to store user passwords or tokens, which significantly reduces the attack surface.
The architecture behind it follows a clear principle: delegation to an app identity instead of a user account to comply with security policies while enabling unattended processes. This is particularly relevant for tasks such as regular site reports, mass changes of authorizations or automated provisioning of new sites.
Technical implementation – explained step by step
1. Register the app in Azure AD
To use App-Only Authentication, you must first register an application in Azure Active Directory. This app is given a unique application ID and is later linked to a certificate.
It is important to assign the permissions correctly: For SharePoint Online, select Sites.FullControl.All from the SharePoint API area, not from Microsoft Graph. The reason: The PowerShell module works directly against the SharePoint endpoints, not against the Graph API.
2. Create and upload a certificate
At the heart of authentication is an X.509 certificate. You can use a self-signed certificate for testing, or a certificate from an internal PKI for production environments. After creation, the certificate is uploaded to the app and the thumbprint is noted. At the same time, you import the certificate into the local certificate store so that PowerShell can access it. The following command is suitable for importing:
Import-Certificate -FilePath "C:\Pfad\zum\Zertifikat.cer" -CertStoreLocation Cert:\CurrentUser\My3. Connect to SharePoint Online
The connection is made via the cmdlet Connect-SPOService. In doing so, you pass the tenant ID, the application ID and the thumbprint of the certificate. A typical script looks like this:
[array]$Domains = (Get-MgOrganization).verifiedDomains
$DefaultDomain = $Domains | Where-Object {$_.IsDefault -eq $true}
$SPOAdminRoot = ("https://{0}-admin.sharepoint.com" -f $DefaultDomain.Name.split('.')[0])Once connected, you can run all of the SharePoint Online module’s cmdlets—without user interaction.
Security Considerations and Architectural Benefits
The switch to app-only authentication is not only a technical improvement, but a security gain. Certificate-based authentication eliminates the risks associated with stored passwords or tokens. In addition, the validity of the certificate can be limited in time, which further increases control over access.
Architecturally, this method fits seamlessly into Zero Trust strategies. The app identity is clearly defined, its permissions are granularly controllable, and authentication is done via a strong cryptographic process. This means that the solution meets both compliance requirements and the demand for automation.
Alternatives and limits
Microsoft recommends using the Graph API for many automation scenarios, especially in conjunction with Managed Identities in Azure Automation. This variant is often more flexible when it comes to accessing user content. App-Only Authentication for SharePoint Online PowerShell, on the other hand, is ideal for administrative tasks such as setting tenant or site settings.
However, there are limitations: some cmdlets might still require user context. Microsoft points out that this is rare, but it is not ruled out. In such cases, the only option is interactive authentication.
Conclusion and outlook
The introduction of app-only authentication for SharePoint Online PowerShell is a long overdue step. It enables secure, unattended automation in environments with MFA and strict security policies. For administrators, this means a considerable relief: scripts can run reliably again without anyone having to intervene manually.
The target-actual comparison clearly shows the progress. Previously, automation under MFA was nearly impossible, but now it’s not only feasible, but also more secure than before. The combination of Azure AD app, certificate, and PowerShell creates a robust architecture that fits into modern security concepts.
The outlook: It is to be expected that Microsoft will continue to expand the functionality and perhaps also check the last cmdlets for app-only compatibility. In parallel, integration with the Graph API will become more important. For you as an administrator, this means planning the transition early, testing certificate-based authentication in a pilot environment and building your automation on it. This ensures that your processes remain future-proof and compliant.
