Ethyl ester (FAEE) production by microbial oil from Mucor circinelloides was investigated by traditional procedure involving the lipid extraction using ethanol followed by transesterification (two-step process) in comparison with directly produce from the whole biomass without extraction (one-step process). Both processes used solid heteropolyacid catalysts (12-molybdophosphoric acid (H3PMo12O40) support on alumina (Al2O3) and niobium oxide (Nb2O5) under conditions previously set up (200 °C for 4h). Although both catalysts provided satisfactory levels of FAEE (>90%), the best performance was attained by H3PMo/Al2O3 resulting in samples that meet the quality standards to be use as biofuel. Regarding the evaluated transesterification procedures, either one or two-steps were able to convert the microbial lipids into ethyl esters with high yields (97%), though the former simplifies the production process due to the elimination of an oil extraction step that incurs oil loss. Moreover, to minimize the energy used for dewatering, this method can be also used for transesterification of wet M. circinelloides biomass. Direct transesterification of wet biomass greatly simplifies the process of FAEE production by eliminating the drying and oil extraction steps, making this a reliable method of great potential.