I was wrestling with my Streamlabs OBS (SLOBS), Voicemeeter Banana, and Windows audio settings for hours before I finally realized the reason why Warframe’s audio was not being picked up in SLOBS.
Endless Google searches led me nowhere, so I had to play around with it myself. Finally, I had an epiphany. Come to find out, Warframe itself actually controls its audio input in the game menu. In your settings menu, go to “audio”, and at the bottom of that menu is an option to select the audio output. Set it to “Voicemeeter Aux Output VAIO”, and it will come through Voicemeeter if you have the correct settings prepared there.
I decided to make this an article on my site with tags that I had used when searching for a solution to this problem, since my own google search results led me nowhere.
I hope this is helpful!