A method of operating a refrigeration system includes initiating a compressor shutdown operation, determining a difference in a saturation temperature at a port of a compressor of the refrigeration system and an ambient temperature and comparing the difference in the saturation temperature and ambient temperature with a threshold. If the difference in the saturation temperature and ambient temperature is less than or equal to the threshold, a pump down operation is performed and if the difference in the saturation temperature and ambient temperature exceeds the threshold, a compressor shutdown operation is completed.