In this study, a factory-integrated recombinant Hirudin downstream process of successive chromatographic purification steps was modified to improve their overall yield. The effect of different ion exchange chromatographic resins for protein capture and altering process conditions was investigated against the yield of the process. The obtained results showed that tuning the pH of the protein solution while keeping the same conventional chromatographic matrix could improve the capture step yield by 5.7% compared to the conventional yield. Further, the particle sizes and internal surface structures of the chromatographic matrices had a significant impact on the yield of the intermediate and polishing downstream steps by 21.2% and 24% respectively. Accordingly, these minor modifications significantly impacted the yield of the production process by a 58% increase compared to the conventional process without affecting any of the critical quality attributes of the product. This change has a significant economic impact, saving 35% of the production cost.