Standalone microgrids utilize renewable energy sources with energy storage devices (ESDs) to supply high-quality power to the load. In this work, a stand-alone DC microgrid is considered, where solar PV is the primary source with battery, fuel cell and supercapacitor as ESDs. Unique characteristics of different ESDs are utilized together in the form of a hybrid energy storage system. It is challenging to distribute and balance the power among source, storage and load together. Therefore, an enhanced energy management system (EMS) for hybrid energy storage-based microgrids is presented with an effective controller to regulate the DC link voltage. A fuzzy-fractional order proportional integral (FOPI) controller is proposed, and a comparative analysis with FOPI and PI controllers is carried out to illustrate the significance of the proposed controller. The simulation study is carried out using the field data for solar irradiance and load profile as well.