In this study the physicochemical properties governing ethylic biodiesel production reactions via homogeneous acid catalysis and waste Brazil nut oil were measured. The behavior of the catalyst, water, and ethanol concentrations in the liquid phase as well as the temperature in both the liquid and the vapor phases and the volumetric flow of the condensed volatile components were monitored during the reaction together with the conversion to biodiesel. The transesterification reactions were induced by microwave heating in a monomode reactor varying the input power to obtain power to sample mass ratios of 1.0-2.25 (W/g) in reactions with 1:6, 1:12, and 1:30 oil to alcohol molar ratios. It was verified that the 1:6 stoichiometric ratio led to higher values for the volumetric flow, the temperatures in the liquid and vapor phases, and the water concentration, along with a greater degradation of the catalyst and reduction in the alcoholic component in the liquid phase. The results indicate that 1:30 is the most favorable molar ratio for the transesterification of waste oils with high FFAs content, providing lower water content and acid degradation. For waste oils, removal of the water is a precondition for the completion of the transesterification process.