A motor controller of an unmanned aerial vehicle (UAV) is optimized to improve operation of the UAV. The motor control optimizations include controlling a motor of a UAV to reduce an operating temperature of the UAV, reducing an amount of latency or jitter resulting from motor operation, and applying a smoothing filter for motor operation. For example, controlling a motor of a UAV to reduce an operating temperature of the UAV can include using a temperature model for the unmanned aerial vehicle or an operating temperature measurement to determine a current operating temperature and comparing that current operating temperature to a threshold. If the threshold is exceeded, settings of the motor are adjusted to cause the motor to operate in a manner that reduces the current operating temperature.