We used a microwave heating system to increase Jatropha biodiesel yield, and to reduce both reaction time and energy consumption. The feasibility of converting natural and non-edible feedstocks including arcuate mussel shells and dolomitic rocks, into a novel high-performance, reusable, low-cost and heterogeneous catalyst for the synthesis of biodiesel was also explored. Arcuate mussel shells and dolomitic rocks were first ground and calcined at 900 ℃ for 2 h. After calcination, calcium oxide (CaO) or a mixed oxide of calcium and magnesium (CaO·MgO) was obtained as white powder, which was then chemically activated to improve the physical, chemical and surface properties, and catalytic activities of the catalysts. By heating CaO from waste shells in an excess dehydrated methanol under 65 ℃ at 8 h with nitrogen (N2) flow, calcium methoxide (Ca(OCH3)2) catalyst was prepared. The CaO from natural rocks was, however, turned into calcium glyceroxide complex, by combining with methanol and glycerol of the by-product. It was determined that calcium glyceroxide (Ca[O(OH)2C3H5]2) was formed during the transesterification and acted as the most active phase. Catalyst characterization was by X-ray diffraction (XRD), X-ray fluorescence (XRF), scanning electron microscope (SEM), energy dispersive spectroscopy (EDS), Fourier transform infrared spectroscopy (FT-IR), and Brunauer-Emmett-Teller (BET) surface area and basic strength measurements. The reaction parameters, including reaction time, microwave power, methanol/oil molar ratio, catalyst dosage and catalyst reusability, were studied for fatty acid methyl esters (FAME) yield. The results indicated that Ca(OCH3)2 and Ca[O(OH)2C3H5]2 catalysts derived from waste shells and natural rocks showed good reusability, high energy efficient, environmental-friendly, low cost and facile route for the synthesis of biodiesel.