The paper evaluated the fate of proteins and carbohydrates in the course of substrate removal by membrane bioreactor (MBR), which was used for the biological treatment of black and grey water components of a controlled decentralized residential area. The MBRs were operated at a high sludge age of 60 days to better observe the magnitude of soluble residual products. Both groups were detected in the raw wastewater and represented 15% of the soluble chemical oxygen demand (COD) content for black water and 9% for grey water. Corresponding ratios in the process effluent were significantly increased to 70% and 24% respectively, indicating that both proteins and carbohydrates were likely to be generated as residual soluble microbial products. Residual soluble organics accumulated in the reactor at much higher levels as compared to the effluent due to cake filtration occurring on the surface of the membrane, entrapping fractions larger than 4-8 nm for proteins, and around 14 nm for carbohydrates. Mass balance showed that proteins and carbohydrates accumulated in the reactor were partially removed due to longer retention and possible acclimation of the biomass. The observed removal rate was much lower for carbohydrates compared with proteins.