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Microsoft Security | Microsoft Graph
An API that connects multiple Microsoft services, enabling data access and automation across platforms
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The Microsoft Graph gives you the raw ability to send a Message in MIME https://learn.microsoft.com/en-us/graph/outlook-send-mime-message so you should be able to use SMIME in theory anyway I've never seen an example of this yet.
The other option for encrypted messaging is Azure Rights Management the Graph can't be used for this as its quite complex and deals with encrypted MSG (OLE messages) but there are specific SDK's if your building an IOS or Andriod apps to help do this.
https://learn.microsoft.com/en-us/windows/win32/srvnodes/rights-management