Abstract: A compartmentalized transport refrigeration system having refrigeration control, and interconnected host and remote refrigeration units for respectively conditioning the air in front and rear compartments of a trailer. The trailer has front and rear doors for access to the front and rear compartments, respectively, and a door switch connected to the refrigeration control which modifies the operation of the refrigeration system when the front access door is opened. When the front access door is opened, the host refrigeration unit is operated in null and the remote refrigeration unit is cycled between heating and cooling modes. A door switch may also be provided for the second access door which modifies the operation of the transport refrigeration system by effectively turning the remote refrigeration unit off.