Separation of cells from produced biomolecules is a challenging task in many biotechnological downstream operations due to deposit formation of the retained cells, affecting permeation of the target product. Compression and relaxation behavior of cell deposits formed during filtration are important factors affecting operational performance. The determination of these factors by flux or pressure stepping experiments is time- and labor-intensive. In this work, we propose a screening method by analytical centrifugation, which is capable of detecting small differences in compression and relaxation behavior induced by milieu changes, using a model system comprised of washed and unwashed yeast cells in the presence or absence of bovine serum albumin as a model target protein. The main effects observed were firstly the impact of pH value, affecting interaction of bovine serum albumin and yeast cells especially close to the isoelectric point, and secondly the effect of washing the yeast cells prior to analysis, where the presence of extracellular polymeric substances led to higher compressibility of the deposited cells. By comparing and validating the obtained results with dead-end filtration trials, the stabilizing role of bovine serum albumin in deposits formed at low pH values due to interactions with the yeast cells was underlined.