A two-stage submerged anaerobic membrane bioreactor (2-SAnMBR) was designed for the treatment of sugarcane vinasse. For start-up, the flow rate was reduced whenever VFA levels reached critical levels in the methanogenic reactor. After acclimation, the system was operated under a continuous flow. Separation of the stages was observed during the entire period of operation. VFA, COD and DOC levels of raw effluent, acidified effluent and permeate averaged 2141, 3525 and 61 mg VFA L-1 (as acetic acid), 15727, 11512 and 488 mg COD L-1, and, 3544, 3533 and 178 mg DOC L-1, respectively. Overall COD and DOC removal efficiencies of 96.9 +/- 0.7% and 95.0 +/- 1.1%, respectively, were reached. Methane content of the biogas from the acidogenic and methanogenic reactors ranged 0.1-4.6% and 60.1-70.1%, respectively. Removable fouling strongly affected filtration performance and cake layer formation accounted for most of filtration resistance. Membrane resistance was related to presence of protein-like substances and carbohydrates. (c) 2013 Elsevier Ltd. All rights reserved.