Starting a year or two ago, Microsoft announced it would stop supporting and/or blocking access to Azure Access Control Services (ACS) and the SharePoint Add-In model. This is important because ACS has been used for many years to grant app/script API access to a SharePoint site(s), and you likely have many sites where this has been used. Moving forward, Azure Access Control (AAC) will be used in place of ACS.

Historically, you would start the permissions journey by generating the client ID and secret at this endpoint:
_layouts/15/AppRegNew.aspx
From there, you grant the newly created identity access to a tenant, sites, lists, libraries, or a combination.
_layouts/15/appinv.aspx
The other option was to create an Azure App Registration and then grant it access to the target objects. When working with SharePoint Online and AppRegNew.aspx, the App Registration is generated automatically. Depending on what is/is not configured, this can be an issue and set off alarms in Azure.

With that out of the way, how do you wire-up a new connection to SharePoint Online, allowing PowerShell, Python, script, or app access to the SharePoint API or the Microsoft Graph API?

Overview of what I’m doing:
Create a self-signed cert
Add the cert to your personal cert store and upload it to Azure, creating an App Registration
Adjust permissions as needed
Grant the App Registration access to a specific SharePoint site
Use the newly created credentials to access the SharePoint site

#create cert with a password
New-PnPAzureCertificate `
    -CommonName "Demo_SP_Azure_2024" `
    -OutPfx c:\code\Demo_SP_Azure_2024.pfx `
    -OutCert c:\code\Demo_SP_Azure_2024.cer `
    -CertificatePassword (ConvertTo-SecureString -String "Taco@Good" -AsPlainText -Force) `
    -ValidYears 1

#import the cert. for this to work, run as Admin.
Import-PfxCertificate `
    -Exportable `
    -CertStoreLocation Cert:\LocalMachine\My `
    -FilePath c:\code\Demo_SP_Azure_2024.pfx `
    -Password (ConvertTo-SecureString -String "Taco@Good" -AsPlainText -Force)

I highly suggest not skipping the ‘-interactive’ part for the next command. It will open a browser window where you must authenticate with an account with adequate permissions to create a new App Registration in Azure. The script’s most important thing to note is SharePointApplicationPermissions Site.Selected. Why is this important? This is extremely useful if you want to limit permissions to a single SharePoint site and not every site in the tenant.

Register-PnPAzureADApp `
   -ApplicationName Demo_SP_Azure_2024 `
   -Tenant tacoranch.onmicrosoft.com `
   -Store CurrentUser `
   -SharePointApplicationPermissions "Sites.Selected" `
   -Interactive

After that runs, the output will include the Client ID and Certificate Thumprint. Take note of it, or you can open Azure, navigate to App Registrations, and select all applications. In the left nav, click Certificates & secrets, where you’ll find the thumbprint; again, in the left nav, click Overview, and you’ll see the Application ID, aka Client ID.

In the next two commands, you will connect to the SharePoint Admin site interactive, then grant the newly created App Registration write access to the target SharePoint site.

Connect-PnPOnline -Url "https://tacoranch-admin.sharepoint.com" `
    -Interactive

#grant the App Reg write access to the site
Grant-PnPAzureADAppSitePermission `
    -AppId 'a95ddafe-6eca-488a-b26a-dc62a64d9105' `
    -DisplayName 'Demo_SP_Azure_2024' `
    -Site 'https://tacoranch.sharepoint.com/sites/cert-demo' `
    -Permissions Write

Now that the App Registration can access the SharePoint site, how do you connect to it using the certificate and thumbprint?

Connect-PnPOnline `
    -Tenant "tacoranch.onmicrosoft.com" `
    -Url "https://tacoranch.sharepoint.com/sites/cert-demo" `
    -ClientId "a95ddafe-6eca-488a-b26a-dc62a64d9105" `
    -Thumbprint "5C5891197B54B9535D171D6D9DD7D6D351039C8E" 

Get-PnPList | Select-Object Title

Using the above commands, you can create a cert, register it in Azure, and grant access to a single SharePoint site.

I’ve included a copy of the full script here:
https://www.sharepointed.com/wp-content/uploads/2024/03/Azure-App-Reg-Cert-Demo.txt

Error(s) and fixes:
Error:
Grant-PnPAzureADAppSitePermission: {"error":{"code":"accessDenied","message":"Access denied","innerError":{"date":"2024-03-21T16:29:47","request-id":"","client-request-id":""}}}
Fix:
Ensure the account running this command Grant-PnPAzureADAppSitePermission , has access to the target SharePoint site.

Error:
Connect-PnPOnline: A configuration issue is preventing authentication - check the error message from the server for details. You can modify the configuration in the application registration portal. See https://aka.ms/msal-net-invalid-client for details. Original exception: AADSTS700027: The certificate with identifier used to sign the client assertion is not registered on application. [Reason - The key was not found., Thumbprint of key used by client: '6C5891197B54B9535D179D6D9DD7D6D351039D8Z', Please visit the Azure Portal, Graph Explorer or directly use MS
Graph to see configured keys for app Id 'eb7f9fbc-f4ee-4a48-a008-49d6bcdc6c40'. Review the documentation at https://docs.microsoft.com/en-us/graph/deployments to determine the corresponding service endpoint and https://docs.microsoft.com/en-us/graph/api/application-get?view=graph-rest-1.0&tabs=http to build a query request URL, such as 'https://graph.microsoft.com/beta/applications/aeb7f9fbc-f4ee-4a48-a008-49d6bcdc6c40']. Trace ID: 3e1e7ab3-60c0-4126-acb8-e2fdb6e28000 Correlation ID: 62ddc80b-aeb2-49c5-8c31-83a04e70bf6e Timestamp: 2024-04-01 12:21:59Z
Fix:
This one is easy; ensure you use the correct Client ID and thumbprint. You can get this from the app registration page in the Azure portal.