Hybrid vehicle embedded systems and payloads require progressively more accurate and versatile thermal control mechanisms and strategies capable of withstanding harsh environments and increasing power density. The division of the cargo and passenger compartments into convective thermal zones which are independently managed can lead to a manageable temperature control problem. This study investigates the performance of a Peltier-effect thermoelectric zone cooling system to regulate the temperature of target objects (e.g., electronic controllers, auxiliary computer equipment, etc) within ground vehicles. Multiple thermoelectric cooling modules (TEC) are integrated with convective cooling fans to provide chilled air for convective heat transfer from a robust, compact, and solid state device. A series of control strategies have been designed and evaluated to track a prescribed time-varying temperature profile while minimizing power consumption. The zone cooling device was tested within an enclosed cabin to provide localized convective zone cooling to a representative heat producing component. Mathematical models for the TEC’s and overall system were developed and validated using these test results. The experimental results demonstrated that an amplitude modulated output from the tracking controller reduced power consumption by more than 78% as compared to a standard thermostat approach while reducing tracking error 19% during an 80 minute test. The findings of this power minimization study indicate excellent power savings opportunities for thermoelectric cooling devices, but also reveal a possible deficiency in current modeling techniques for thermoelectric devices.