The beamhouse sections of tanneries produce around 45% of the total wastewater of factories. A beamhouse wastewater, collected after the oxidation of sulphide compounds and diluted to average COD and ammonium concentrations around 550 and 90 mg/L respectively, was treated separately in two reactors: a sequencing batch reactor (SBR) and a membrane sequencing batch reactor (MSBR). Both systems were operated for 150 days with similar conditions without sludge purge, operating at low feed to microorganisms (F/M) ratios and applying organic and ammonium loading rates up to 0.75 gCOD/L·d and 0.12 gNH4+/L·d respectively. The SBR achieved low ammonium and nitrogen removal rates and COD removal values close to 90%, which decreased dramatically during the last 30 days of operation. An important washout of microorganisms in the SBR was noticed due to the proliferation of filamentous bacteria. However, removal efficiencies close to 100% in ammonium and 90% in COD were achieved in the MSBR, and very stable operation was maintained.