Membrane enhanced peptide synthesis (MEPS) combines liquid-phase synthesis with membrane filtration, avoiding time-consuming separation steps such as precipitation and drying. Although performing MEPS in a multi-stage cascade is advantageous over a single-stage configuration in terms of overall yield, this is offset by the complex combination of operational variables such as the diavolume and recycle ratio in each diafiltration process. This research aims to tackle this problem using dynamic process simulation. The results suggest that the two-stage membrane cascade improves the overall yield of MEPS significantly from 72.2% to 95.3%, although more washing is required to remove impurities as the second-stage membrane retains impurities together with the anchored peptide. This clearly indicates a link between process configuration and operation. While the case study is based on the comparison of single-stage and two-stage MEPS, the results are transferable to other biopolymers such as oligonucleotides, and more complex system configurations (e.g. three-stage MEPS).