The mechanistic modeling of biodiesel production process in membrane reactor with the consideration of chemical reaction, phase equilibrium, and ultrafiltration is important for the membrane reactor design. In part II of this work, the chemical and phase equilibrium (CPE) model for crude palm oil transesterification reaction in the membrane reactor developed in part I is extended to an integration of CPE with modified Maxwell-Stefan model, which considers multicomponent mass transport phenomena of concentration polarization and intramembrane. A good fit of simulated permeate fluxes and apparent solute rejection to the experimental data shows that the model has a good prediction capability. Reversible fouling was found to be the major fouling and no pore plugging was observed. Simulation results verified that micelles were retained by the membrane at CPO:MEOH molar ratio of 1:24 and catalyst concentration of 0.5 wt %. However, phase inversion happened when catalyst concentration of 0.05 and 0.1 wt % were used. (c) 2015 American Institute of Chemical Engineers AIChE J, 61: 1981-1996, 2015