A low-intensity ultrasonic measurement system was used to monitor the products of transesterification of soybean oil in methanol to FAME (biodiesel). The byproducts of the transesterification reaction are methyl esters, glycerol and other products. During the transesterification reaction, the glycerol, having a higher density than the methyl ester, settles at the bottom of the reaction vessel. The aim of this study was to measure the glycerol deposition rate during transesterification and to assess the reaction rate and end time. Soybean oil was converted into biodiesel at four temperature levels. The amount of catalyst (KOH) used in the transesterification reactions was determined by titration. The ultrasonic waveforms captured during the reaction were recorded and analyzed automatically. The ultrasonic system monitored the effects of reaction temperatures on the glycerol settling rate and the reaction end times. The ultrasonic measurement of glycerol settling would be a useful non-destructive method for evaluating the effects of parameters such as catalyst amount, mixing time and temperature on transesterification reactions.