This paper proposes an electric energy management system (EEMS) based on the particle swarm optimization (PSO) technique that can provide enhanced effectiveness in the appliance scheduling and energy storage control of a nearly zero energy building (nZEB). Specifically, the PSO online finds the optimal operating condition by properly time shifting the controllable loads of a nZEB and regulating the direction of the energy flow and the current of the electric energy storage system (EESS). Therefore, shaving of the consumption peaks of the household energy demand as well as improved exploitation of the energy storage capability and protection of the lifespan of the EESS are accomplished. The above both provide efficiency increase and enhancement of the stability and the seamless operation of the nZEB electric microgrid. The EESS consists of Li-ion batteries. The effectiveness of the proposed EEMS is evaluated by using a hardware-in-the-loop (HiL) simulator that consists of a microcontroller board of ST that houses the control software and the DS1104 controller board of dSPACE that accommodates the models of the renewable energy sources (RES), the EESS with Li-ion batteries and the electric loads of the nZEB. The developed HiL provides a comparable advantage that is the easy adaptation to any potential changes of the layout of the nZEB microgrid. In order to validate the feasibility and demonstrate the competitive advantages of the EEMS as well as the effectiveness of the developed HiL, several testing results are presented and discussed.