Although integrating the thermoelectric device (TED) to fuel cells (FC) is a promising way to improve the overall system’s output efficiency, its application to the micro-combined heat and power (μCHP) application requires an effective energy management strategy. Therefore, this paper aims to develop a real time energy management strategy (EMS) that intelligently allows the FC and TED to cooperatively minimize primary energy consumption and startup time while properly balancing energy in the energy storage components. This EMS is unique in that it includes TED’s mode of operation and FC and TED’s operating powers as controller parameters for a multi-input multi-output (MIMO) controller. As such, it regulates FC and water tank temperatures and the electric battery’s state of charge. The proposed overall system is tested under 3 dynamic simulations that include startup from ambient and satisfying the energy demands during a winter and summer day. Results demonstrate that adding the TED has reduced startup times by up to 4.45 and 1.77 times for the 1 kW FC stack and 50 kg water tank respectively. Primary energy consumption efficiencies also improved by up to 3.4% in winter and 5.6% in summer when the TED is included into the system.