A system and method for controlling double transition shifts in an automatic transmission having multiple gear sections. During a double transition shift, the system performs simultaneous closed loop control of the primary oncoming clutch in the primary gear section and the secondary off-going clutch of the secondary gear section. Before the input shaft of the secondary gear section is fully pulled down or the secondary off-going clutch becomes overheated, the system switches closed loop control of the input shaft to the secondary on-coming clutch of the secondary gear section. The system utilizes model-based calculations to determine the initial clutch pressure settings when a clutch enters closed loop control.