Whey protein fractionation was carried out at laboratory scale by applying the required temperature and pH conditions in a standard configuration batch agitated vessel to cause selective precipitation and aggregation of proteins. Scale-up of this operation to pilot scale was achieved on the basis of impeller power input per unit volume resulting in similar particle sizes. Separation was subsequently achieved by high-speed disc-stack centrifugation. Processing of precipitates in pumps, valves and at the centrifuge inlet zone can lead to substantial breakage, depending on the strength of the precipitates formed and aged in the batch vessel. Such turbulent processing was mimicked at lab scale by passing the precipitate solution through a ball-valve rig while monitoring the effects on particle size and fractal geometry. Measurement of fractal dimension were used to assess the compactness of precipitates. Precipitates subjected to higher batch vessel impeller shear-rates during formation and ageing were found to be smaller, more compact and better able to resist turbulent breakage and thus should provide better feed-stock for disc-stack centrifugation at pilot scale. Clarification efficiency curves obtained for pilot-scale disc-stack centrifugation confirmed these lab-scale predictions. Recommendations for improved process design in terms of selecting suitable batch vessel shear-rates that ultimately lead to improved separation efficiencies have been made.