Energy storage devices and renewable resources especially rooftop photovoltaic (PV) are vital in operation of nanogrids. In this study, energy management strategy (EMS) for battery energy storage system(BESS), PV, super-capacitor (SC) is presented. The proposed control strategy is designed to optimize BESS flow rate, discharge and charge cycles energy system using Meta-heuristic Jaya algorithm by properly coordinating SC and PV. SC was employed in HESS to fulfill the transient energy mismatches and reduce the transitory high charge/discharge impact on BESS using EMS. The proposed controller also has the benefit of keeping the battery’s SoC within limitations for a long period. In order to extend the life of BESS, the EMS is aimed at minimizing deep charging and discharging. PV generation is reduced, particularly under light load (no-load) situations and when battery SoC ≥ SoCmax. Similarly, SC charging and select able load shedding are employed when SoC ≤ SoCmin to avoid deep discharge. This controller method is validated in both simulation environment and hardware-prototype under different perturbation and operating conditions.