This work improved the fatty acid methyl esters (FAMEs) quality produced using a stoichiometric methanol to oil molar ratio, removing monoglycerides (MGs), diglycerides (DGs) and glycerol by using a ceramic membrane. This work improved the conventional biodiesel batch reactor (CBR) performance, adding a refining stage using a ceramic membrane according to two different operational strategies: a batch reactor membrane system (CBR-MS) and a sequential batch membrane reactor (SBMR). The SBMR strategy showed the best results with an 87. wt.% FAME conversion yield and a 99.9% glycerol removal efficiency. SBMR was based on the operation of consecutives cycles of charge, transesterification, and discharge of permeate by operating the membrane only when a 70% FAME conversion was reached. This allowed both to work with a low viscosity product, increasing the permeate flux during the filtration process, and to diminish MG and DG content in the permeate. The application of the SBMR strategy improved a 34% the FAME content in the final product, in comparison to the CBR and 13% in comparison to CBR-MS. In addition, MG content was reduced a 79% in the final product in comparison to the CBR and a 20% compared to the CBR-MS. Finally, the DG content was reduced a 78% in comparison to the CBR and a 50% compared to the CBR-MS system when applying the SBMR strategy. It is proposed that the biodiesel successful separation-refining performance depends on the evolution of the emulsion during transesterification, as the ceramic membrane cannot remove MG and DG, but using the adequate strategy, their removal is possible from the biofuel stream.