Distributed Generation (DGs) are emerging as a favorable and eco-friendly solution for energy production. DG systems typically consist of small to medium-sized power-generating units, such as solar panels, wind turbines, fuel cells, or microturbines, which are integrated into the local power grid or used independently. However, because renewable energy sources are inherently variable, they pose challenges and operational difficulties when used as the sole energy source. To overcome these issues, it’s essential to incorporate energy storage systems and carefully manage the uncertainties associated with both energy demand and generation. This paper proposes a structure of system that connects wind energy, solar (PV), Fuel cell (FC) and Battery Energy Storage System (BESS) in a Multi-Microgrid (MMG) structure. This study gives the analysis to address the uncertainties in energy demand, weather conditions, and cost of energy, optimizing the arrangement of DGs and BESS within the MMGs. To find the optimal location and sizing of DGs for the MMG system, the Jaya optimization algorithm is employed. The use of Jaya optimization has resulted in a reduction of the Net Present Cost from $451.354 million to $434.256 million and the Levelized Cost of Energy (LCOE) to $0.267 per kWh, taking into account the uncertainties in energy demand, generation data, and fluctuating energy prices. The effectiveness of this approach is confirmed by comparing the results with those obtained using the GWO algorithm and CCPSO algorithm,. The Jaya algorithm shows superior performance, achieving lower total NPC, reduced system size, and a lower LCOE, while also exhibiting the fastest convergence, making it more accurate and reliable than the GWO and CCPSO, PSO algorithms.