I am successfully able to deploy nodejs application in azure app service.

I also able to deploy nodejs against multiple virtual application in azure app service. To run multiple nodejs application against virtual application I have to deploy complete folder into new folder path and map it to virtual application. I want to achieve it with single physical folder only.

Let me give a sample below.

Sr.No     Virtual Application             Physical Path
1.        /dev1/App                        /wwwroot/dev1/App
2.        /dev2/App                        /wwwroot/dev2/App

I could able to achieve the above scenario.

I am trying to achieve the below one.

Sr.No     Virtual Application             Physical Path
1.        /dev1/App                        /wwwroot/a/b/app
2.        /dev2/App                        /wwwroot/a/b/app

I am using iisnode + web.config.

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In short, it's impossible.

You can deploy multiple projects in single azure web app like the first scenario you provided.

A virtual directory is a directory name (also referred to as path) that you specify in IIS and map to a physical directory on a local or remote server. The directory name then becomes part of the application's URL, and users can request the URL from a browser to access content in the physical directory.

If you host multiple virtual app with a single physical directory, it is more difficult to discover the actual physical file structure on your server because the URL does not map directly to the root of the site.