We have received a few cases in AAD Audit Log support topic around AAD audit logs showing a service principal named “Microsoft Substrate Management” has created users in their AAD tenant and they have no idea who this principal is.
You can find this service principal in your tenant using AzureADPreview Powershell module and the following cmd:
Get-AzureADServicePrincipal -Filter "DisplayName eq 'Microsoft Substrate Management'" | fl *
Where you should be able to confirm this is a 1st Party principal (PublisherName = Microsoft Services) with AppID = 98db8bd6-0cc0-4e67-9de5-f187f1cd1b41
After investigation, it was determined that the “Microsoft Substrate Management” service principal is a 1st party service principal used by Exchange Online during dual write operations to AAD. When for example a mailbox is created directly in Exchange Online, this service principal may show up in your audit logs as the actor who created the user account the mailbox will be assigned to.
More information on dual write operations in Exchange Online can be referenced at https://techcommunity.microsoft.com/t5/exchange-team-blog/exchange-online-improvements-to-accelerate-replication-of/ba-p/837218
For a better picture of the actor who initiated the request in Exchange Online, you will need to search the Office 365 Unified Audit Log in the timeframe of the activity via steps mentioned in the following articles:
Hope this helps someone!