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A boost-cascaded-with-buck converter-based power conditioning system employing a seamless mode transfer maximum power point tracking controller is proposed to maximize energy production of a thermoelectric generator while balancing a vehicle battery, alternator output power, and vehicle load. When a vehicle battery is fully charged, the proposed controller switches to a power matching mode seamlessly by a dual loop control system, which detects the input and output voltages and currents of the boost-cascaded-with-buck converter, and adjusts the commands accordingly. Both voltage and current loops are designed in a frequency domain using small signal models to ensure stable operation. A mode selection and voltage and current commands are determined by a digital signal processor-based controller. The experimental results with a dynamic source and load steps are presented to show the effectiveness of the proposed approach.