Christian Béland
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After multiple attemps, I got it to work. It is just not documented.
You have to:
1 - Create the private endpoint in Atlas (vnet name should be "default" or use az cli to find out)
2 - Note the connection string to connect to the private endpoint in mongodb:// format (ex: mongodb://USERNAME:PASSWORD@PRIVATE-ENDPOINT-HOSTNAME:1033,PRIVATE-ENDPOINT-HOSTNAME:1034,PRIVATE-ENDPOINT-HOSTNAME:1035/?ssl=true&replicaSet=REPLICATSET-NAME&authSource=admin&retryWrites=true&w=majority)
2- Create a managed private endpoint of type "Private Link Service" in ADF and add the PRIVATE-ENDPOINT-HOSTNAME in the Fully Qualified Domain Names list
3- Create the MongoDB Atlas Linked service using a private integration runtime and the aforementioned connection string.
Hope this helps!