I have a simple web API 2.0 that I want to host in azure websites. Do I need owin for this or does owin only make sense when you are using Azure Web worker?
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A Web API based on Owin works just fine in Azure Web Apps, as long as it's configured to be IIS-hosted. You do not have to use Owin of course.
Here's a related question and answer: Owin app in Azure