To produce biodiesel from used cooking oil and other nonedible feedstocks such as coffee oil and algae oil, a phosphotungstic acid loaded KIT-5 (Korea Institute of Technology-5) catalyzing methanol process was developed. Kinetics studies show that a simple catalytic mechanism describes the kinetics of the esterification kinetics. The catalysts used were mesoporous materials with active sites concentrated on their surface, thereby eliminating the need for free fatty acids diffusion through the pores, while providing rigidity through the layered structure. The Damköhler number was found to be in the range of 0.01–0.08 which suggests that the reaction is independent of the diffusion rate. Further, the effect of process variables including temperature, catalyst loading, surface area, volume ratio of alcohol and oil, mass of the catalyst and time on fatty acid methyl esters yield were also investigated. It is found that the temperature of the system does not affect the conversion significantly within the range studied. From experimental data analysis on the proposed mechanism, we determined the activation energy (Ea) to be 50.6 kJ mo1–1 with a pre-exponential factor (Af) of 5.6 × 105 min–1 for the Arrhenius form.