The Microsoft Graph request me/messages does not only contain emails but also Skype chats (from the folder conversation history) and Microsoft Teams chats.
I have set up a Microsoft Graph Webhook to monitor changes in messages, it works fine for emails and Skype Chat but not for Teams Chat, I do not receive notifications when a new Chat is sent.
By Skype, you mean Skype for Business. That's because Skype for Business archives chats into the user's inbox.
Teams does archive all chats into the user's Exchange inbox for e-discovery/retention/legislative hold features in certain SKUs of Office 365, but they are not stored in the IPM Subtree portion of the user's mailbox which is where webhooks come from.
In other words, this won't work, and that's by design.
We will be supporting this capability via dedicated APIs for Teams in Microsoft Graph but we have not yet announced a timeframe.
