Recovery of recombinant proteins produced intracellularly 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 cell debris using centrifugation or tangential flow filtration. Often a precipitation or floculation 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). Previous work by our group has successfully demonstrated the characterization and improvement of centrifugal clarification with E. coli suspensions, yeast suspensions and protein precipitates using an ultra-scale down methodology. The major benefit of this approach is the use of a predictive scale down model that enables rapid optimization of operating conditions with only small volumes of material required. This study expands the application of the technique to a concentrated E. coli extract that has been flocculated prior to the centrifugation step. Results obtained show that, with proper theoretical and experimental consideration to account for high cell density, clarification performance in the laboratory is in good aggrement with pilot-scale data. More optimum flocculation conditions were also identified that resulted in enhanced clarification at pilot scale.