Setting EF Connection String in Azure Web App

The problem is the escaped quotes: ".

The connection strings in web.config have quotes escaped because they are serialized in an XML attribute. When entering a connection string in the Azure portal you should provide the raw unescaped string. Something like this:

metadata=...;provider connection string="Data Source=..."

David Ebbo's answer is good for confirming that the Environment is set up as you expect. It is also helpful to pay attention to the .pubxml file when publishing via the wizard in Visual Studio: it will try to populate connection strings as well.

'custom' should be correct here. In that case, the providerName is left unchanged, so if you have System.Data.EntityClient in your config, that should remain after the Azure runtime changes it.

Try going to Kudu Console and click on Environment to make sure the conn string looks correct there.