Abstract: Methods and systems for controlling the operation of the condenser and evaporator fans in a transport refrigeration system are described. The methods and systems described herein generally control dynamically a plurality of system fans needed to meet a plurality of system airflow objectives, where the objectives may sometimes be conflicting. The methods and systems described herein can be used to strike an optimal balance between system performance, protection, safety and regulatory requirements. In some embodiments, the systems and methods described herein provides for controlling the operation of at least two condenser fans based on the difference between a coil temperature (e.g., discharge pressure temperature saturation) and an ambient temperature and controlling the operation of at least one evaporation fan based on an air temperature differential.