A system and method for controlling a transport heating, ventilation, and air conditioning (HVAC) system having a fresh air intake is disclosed. The fresh airflow intake system includes a fresh air damper configured to regulate a flow of fresh air into the transport HVAC system, an evaporator fan having at least a high-speed mode and a low speed mode, and a controller. The controller is configured to determine whether a fresh air condition is met and increase a fresh airflow in response to determining the fresh air condition is met. The controller is further configured to increase an evaporator fan speed when the fresh airflow is increased.