Two different membrane treatment scenarios have been applied for treatment of the high strength dark color alkaloid industry wastewater. A membrane bioreactor (MBR) system having separately UF and MF membranes was operated with raw alkaloid wastewater treatment (scenario-A) and anaerobically pre-treated alkaloid wastewater (scenario-B). NF 270, NF 90 and RO (XLE) membranes were used as a polish-ing step at two different recovery ratios of 50% and 75% for both scenarios. In scenario-A, the COD re-moval efficiencies for MBR-MF and MBR-UF were found as 86±9% and 55±24%, respectively. At the polishing step, RO performance after scenario-A indicated that the 99.6% COD and complete color remov-al was achieved. On the other hand, in the scenario-B, the COD removal efficiencies for MBR-MF and MBR-UF were found as 41±16.4% and 24±18.3%, respectively. RO experiments with raw wastewater indi-cated that the 99.6% COD and complete color removal were achieved. The most crucial problem during direct MBR operation was found as a foaming problem and prevented by anti-foaming agent which caused an increase in effluent COD concentration and chemical cost. For these reasons, it can be concluded that MBR operation with anaerobically pre-treated was more effective than the other scenario.