The nature of solar irradiation and wind velocity is continuously varying and uncertain. The power generated by Distributed Generators (DGs) such as solar panels and wind mills using this source is also varying continuously. The power variation in distributed generation (DGs) needs to be controlled before connecting to the load. To maintain the autonomous microgrid, the Fuzzy Logic Controller-based Energy Management System (FLCEMS) is developed and implemented in the simulation. FLCEMS consists of three fuzzy logic controllers (FLC) that help achieve a proper control strategy. FLCEMS is implemented in Energy Control Center (ECC) and consists of three FLCs for fuzzy decision-making, fuzzy mapping, and a fuzzy control system to handle all uncertainty in the microgrid system. The FLCEMS are implemented between DG and EMS to achieve adequate control and monitoring strategy of autonomous microgrids. Using this approach, monitoring and effective control of autonomous microgrid in ECC. The results show that the effective utilization of Solar PV panels and windmills is enhanced by using the FLCEMS approach.