The aim of this study is to develop a membrane-based treatment scheme to remove colorants from the effluent of a baker's yeast plant. For this purpose microfiltration (MF), ultrafiltration (UF) and nanofiltraton (NF) membranes with differing molecular weight cut-offs (MWCOs) were tested. To evaluate the effectiveness of membrane processes in treating the waste stream, optical density (OD), COD, color measurements together with permeation fluxes were used. Effects of pretreatment methods (coagulation and coarse filtration) and feed composition on OD, color, COD were studied. In addition, gel filtration analysis was employed to characterize feed and permeate streams in terms of MW distribution of organics that are present. Maximum rejections obtained were 94%, 89% and 72% for OD, color and COD, respectively, when 0.8 microm microfiltration membrane and 400 Da NF membrane were used in series. It was also observed that addition of intermediate UF steps did not increase overall rejections and final permeate flux of NF membrane. Based on these observations, an efficient scheme was offered.