A system for dynamically mitigating resonance in a transport refrigeration unit (TRU) during a mission, having: a TRU controller configured for operating a TRU engine during the mission according to an operational baseline, and while operating the TRU engine, contemporaneously performing steps including: obtaining a first set of data that comprises real time measurements from one or more accelerometers installed in the TRU; converting the real measurements to a second set of data that comprises real time shock and vibration data; processing the second set of data in a control loop to determine an updated operational baseline that avoids resonance detected in the first set of data; and operating the TRU engine according to the updated operational baseline.