I can answer in terms of API management. To provide a connection between the Mgmt API and your backend (sometimes called last mile security), there are several options:
- Basic Authentication: This is the easiest solution.
- Mutual certificate verification: https://azure.microsoft.com/en-us/documentation/articles/api-management-howto-mutual-certificates/ is the most common approach.
- IP White List: If you have an instance of APIM Standard or Premium, the IP address of the proxy server will remain constant. This way, you can configure firewall rules to block unknown IP addresses.
- JWT token: if your backend has the ability to check JWT tokens, you can block all callers without a valid JWT.
This video may also be useful: https://channel9.msdn.com/Blogs/AzureApiMgmt/Last-mile-Security
I think the document meant that you could do a JWT token check in APIM. However, so that someone does not directly access your server, you will have to implement one of the options mentioned above in Api Apps
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