When I first turn on my mini it makes a weird knocking noise from the engine bay, it's very rapid sounding, once the motor is warmed up for a minute or so the noise completely goes away, it seems to do it more when the car sits for more than a few days I noticed.

Any thoughts on what it is?

 

By chance have a video? What side of the motor does it seem to be coming from? It is super cold weather where you are? Could just be some timing chain noise.

 

My best advice would be to get the car to a qualified Mini shop for a professional Mini mechanic's diagnosis. Unlikely even if you learn what the noise is that you could do much about it on your drive way.

Even with an audio clip accurate diagnosis of any noise is more guesswork than science. And I'm not suggesting you make an audio clip. My advice is as I said above: Get the car to a professional. He can pinpoint the source of the knocking and from this make a high confidence diagnosis as to its cause.

A knocking noise I heard from my 2002 Porsche Boxster, a deep kind of muffled knocking, a knocking not in sync with engine RPMs, was coming from a loose converter "brick" in the exhaust manifold. It would knock when cold then buzz when up to temperature. Once in a great while the converter would trigger a CEL and a P0430 error code.

At other times, with my other previous car, a Porsche 996 Turbo, once the engine/transmission (6-speed manual) was up to temperature and I'd roll up to a stop slipping the transmssion into neutral and releasing the clutch pedal I'd hear an irregular knocking noise. A press of the clutch clutch pedal followed by a release would have the noise gone. The noise was due to the slight irregular idle speed of the Turbo engine and this would cause some rattle (knocking) in the transmission. Subsequently at some point after I replaced the O2 sensors, then later the plugs and coils (and in both cases the engine ran a bit better afterwards) the transmission knocking noise was gone. My assumption is the engine was a bit out of "tune" and this accounted for a bit rougher engine idle.

Of course there are a number of other possible explanations some rather minor to deal with others not so minor to deal with/address. So you really want to be sure of the diagnosis before you move forward.

 

Moving you to the Stock Problems/Issues area.

With long distance diagnosing the more information you can provide the better chance the darts we throw will hit on your issue. What year? How many miles? Auto or stick? Make the sound when in gear or out of? When was the oil changed last? What side, right of left etc etc etc