Your post isn’t clear. You say the microphone isn’t working properly but how do you know? Do you mean that the recipient of you call can’t hear you very well, that is different.
To be clear, do you have the 0084 update which was designed to fix the audio on phone calls not WhatsApp. This is an ongoing issue and is not a microphone problem per se. You can check the microphone via the phone call keypad.
*#*#66#*#* >Service tests > Test single > Microphone
There are two mics and the second one is the noise cancelling mic and is quite.
It seems that often, for some people, when using WhatsApp, a previous demand for the main Microphone 1 is not released and so only the top microphone for noise cancelling is being used resulting in a very low volume at the recipients end.
As I said this seems due to other apps not letting control of the main mic so you may want to disable other apps that may intertere, ~ I removed a recording app ~ and reboot the phone. Try a WhatsApp call again before you re-enable other apps and you main find the issue.
This clearly shouldn’t happen and Fairphone will need a few requests from users to take it an important issue to resolve software wise.