Unfortunately not all microphones or headphone adaptors work with the iPad headphone / microphone four pole socket. Sometimes the order and timing in which the adaptor is plugged in affects whether the external adaptor is recognised. Sometimes the work and sometimes they don't! Try downloading Recorder Plus HD (free) which has a panel telling you what microphone is currently in use (internal, headphone socket or USB) to confirm microphone selected and then try plugging the adaptor in well before and alternatively well after starting GB and confirm microphone selected with RPHD. The apps may need relaunching and restarting the iPad can help. It is a bit hit and miss in my experience.
What ipad, iOS and adaptor are you using? Microphones, line input and guitars require different impedance inputs and thus different input devices. An adaptor 3.5 mm to 1/4" almost certainly won't work. Cheap adaptors might which separate the socket into headphone and microphone lines might or might not work. Special adaptors by IK Multimedia and others and others work but the headphone / microphone inputs tend to suffer from crosstalk in my experience. An external adaptor plugged into the 30 pin or lightning port (e.g. Line 6 Sonic Port, IK Multimedia iRig or Behringer is202) is the most reliable and highest quality option.