This study investigates the conversion of marine microalgal oils into biodiesel using a microwave-assisted process with transition metal catalysts supported on natural waste materials. The aim is to enhance the efficiency and sustainability of biodiesel production while addressing environmental challenges associated with fossil fuels. Waste-derived materials, particularly banana peels, were used as eco-friendly, cost-effective catalyst supports. Key objectives included developing novel catalysts, optimizing reaction conditions (microwave power, catalyst loading, methanol-to-oil ratio, and reaction time), and characterizing the catalysts. Five catalysts—Ni/KOH-from banana peels, Ni-Ag/KOH-from banana peels, Ni-W/KOH-from banana peels, Ni-Co/KOH-from banana peels, and Ni-Mo/KOH-from banana peels—were synthesized using the impregnation method with a fixed 10 wt.% metal loading. Several techniques such as N2-physisorption, X-ray diffraction (XRD), scanning electron microscopy (SEM), and thermogravimetric analyzer (TGA) were applied to characterize the catalysts. The impact of microwave irradiation on accelerating reactions and reducing energy consumption compared to traditional methods was also explored. The controlled synthesis has resulted in a series of catalysts with a high surface area (~220 m2/g). Microwave-assisted transesterification achieved a 97% selectivity using Ni-W/ KOH-from banana peels catalyst under optimized conditions (0.6 kW microwave power, 1.0 wt.% catalyst loading, 10 minutes reaction time, and a 15:1 methanol-to-oil ratio). Additionally, the Ni-Mo/ KOH-from banana peels catalyst achieved 92% selectivity at 0.8 kW microwave power, 0.5 wt.% catalyst loading, 5 minutes reaction time, and a 15:1 methanol-to-oil ratio, demonstrating the synergistic effects of transition metal combinations. These results highlight the potential of banana peel-derived catalysts combined with microwave technology as a cost-effective and sustainable approach for biodiesel production. The findings contribute to advancing clean energy technologies and provide a scalable, environmentally friendly pathway for renewable fuel synthesis.