The refractory substances and foulants are the main hindrance in treatment of many organic effluents. The aim of the study was to characterize the distribution of COD particles in molasses distillery wastewater (MDW) and their effects in membrane fouling. The factors analyzed include: permeate flux, conductivity, trans-membrane pressure, pH, color, biochemical oxygen demand (BOD), chemical oxygen demand (COD), and total nitrogen (TN). Further analysis was done using high performance liquid chromatography (HPLC) and the liquid chromatography–organic carbon detection (LC–OCD) technologies. The permeate flux and permeability for 100kDa membrane test were found to increase with time when the feed was not pre-filtered with Whatman paper. This was caused by the abrasion effects of huge particles on the active surface of the membrane. The microbial products were found to play a significant role as foulants for the digested effluent. A possible treatment process for MDW would start with biological digestion followed by microfiltration to remove huge particles before ultrafiltration and finally nanofiltration. The process eliminates more than 80% remnant COD and increases its BOD5/COD ratio from 0.07 to 0.3. An alternative process should entail membrane pretreatment of raw MDW before anaerobic digestion with 50kDa membrane because of its reasonable permeate flux.