The objective of this study was to determine the effect of increased temperatures on atmospheric pressure transesterification reaction rates, reaction rate changes due to the possible mixing benefits of a cyclonic separator, and to perform emission level comparisons between petroleum-based diesel fuels and methyl esters. In order to facilitate these tests, the capabilities of the biodiesel pilot plant in the BECON energy center were expanded to include on-site soybean oil production and processing, temperature-controlled transesterification reactions, recirculating cyclonic separation capabilities, on-site diesel electric power generation, and NOx and smoke emissions testing. The results of the reaction rate temperature tests indicate that atmospheric pressure transesterification reactions can be driven to completion in less than 22 minutes using a sodium methoxide catalyst. The preliminary investigation of the cyclonic separator mixing effect showed increased reaction temperatures resulted from recirculating through the separator during transesterification. Further investigations into the separating characteristics and optimum mixing schedules are necessary in order to better use this technology. Exhaust emissions comparisons between biodiesel and petroleum-based diesel fuels showed an average 10% increase in NOx for biodiesel-based fuels at 80% of maximum engine power but an 11% decrease in NOx emissions at 100% of maximum engine power. Smoke tests showed significantly reduced particulate emissions for biodiesel at all operating conditions with an average 27% reduction at 80% of maximum engine power and a 54% reduction at 100% of maximum engine power. Exhaust gas temperatures were reduced under all operating conditions for the biodiesel-based fuels as compared to the petroleum-based fuels.