The recovery of intracellular recombinant proteins produced in microbial systems typically requires physical, chemical or thermal treatment of the cells post-harvest to release the product into the broth, followed by removal of the cell debris using centrifugation or tangential flow filtration. Often a precipitation or flocculation step is introduced to facilitate the liquid-solid separation. Due to the complex nature of the cell materials and the unit operations, it is difficult to obtain data at laboratory scale that closely reflect the performance of these operations on larger scales (pilot or manufacturing). This study uses a predictive scale-down model that enables rapid optimization of the operating conditions for a flocculation followed with a centrifugation step using only small volumes (20 mL) of a high solids (∼20% w/w) E. coli heat extract. Results obtained show that, with proper theoretical and experimental consideration to account for high cell density, conditions could be found that improve the beneficial interaction between flocculation and centrifugation. These experiments suggested that adding a higher level of a cationic polymer could substantially increase the strength of the flocculated particles produced, thereby enhancing overall clarification performance in a large scale centrifuge. This was subsequently validated at pilot scale.