I am running into this issue with my Canon EOS M3 where for some reason no matter what external microphone I use, it always uses the M3's internal microphone. I've been trying everything and looking up possible fixes, but I cannot seem to find a solution. I even tried to reset the camera settings, but it wouldn't let me as it said the device was busy. Thank you for any help with this.
The M3 should recognize the 3.5mm mini audio plug and record from that instead of your internal mic. I did a quick scan of the manual and did not see any custom function that would override this. The fact that it records audio from the internal means the jack doesn't even recognize that anything is plugged into it. So it sounds like hardware failure to me not a user issue. Did it use to work and stopped suddenly? I would contact canon, they may have had a batch with faulty mic jacks.