I have been having the same problem. It turns out (in my case), that if I plug a headset with a microphone in, then it works. If this is the case for you too, it could be a hardware problem. The microphone is located on the backside of the USB-C side board. I ordered a new one and installed it today. Thankfully it fixed the issue and the (new) internal microphone is now working.

Instructions: To replace the USB-C side board, you need to follow steps 1-5 of replacing the main board. Then the USB-C side board is glued in place, as explained in the note about the vibration motor.

Note: Doing the replacement yourself is a bit fiddly and requires the right precision tools, but definitely doable.

• USB-C side board replacement: https://pine64.com/product/pinephone-usb...
• Steps 1-5 replacing the main board: https://wiki.pine64.org/index.php/PinePh...