Robust and accurate modelling of bioprocess systems offers the opportunity to visualise strategies for rapid-scale up of production platforms from benchtop to industrial scale, but few studies investigate how mechanistic and hybrid models can be used to design integrated bio-manufacturing. This is especially true for downstream purification technologies used to separate mAbs from culture by-products, e.g. host cell proteins. Polishing chromatography (cation-exchange mode) is commonly used to remove these by-products, but optimal bind and elution operation of these columns is complex. Ultrafiltration is typically applied in conjunction with diafiltration post-polishing chromatography in order to obtain suitable final product titers and excipient concentrations. This study presents a combination of dynamic models to probe batch polishing chromatography and ultrafiltration operating strategies achieving industrial specifications for recovery yield and mAb titer. A series of elution and filtration strategies are implemented, resulting in a total of 40 flowsheets explored. A steric mass action model with 7 pH-dependent parameters is employed to simulate scale-up polishing chromatography column behaviour. Moreover, a published gel layer ultrafiltration model based on Darcy’s law is implemented to purify the outlet of the polishing chromatography column. Strategies that are successful in achieving the target 90% recovery yield and 100 g L−1 concentration specifications are compared via a comprehensive analysis, to deduce the operational protocols which offer minimised salt consumption and pressure drop whilst respecting design criteria.