Colloidal filtration processes using porous membranes suffer from productivity loss due to colloidal matter retention and continuous build-up by the retained matter. Especially during filtration of soft matter, the deformation of the individual colloids that make up the filter cake may be significant; however, this deformation and its impact remain unresolved so far. Yet, understanding the deformation on the single colloid level as well as on the ensemble level is important to be able to deconvolute filter cake properties from resistance increase of the membrane either by simultaneous internal adsorption or blocking of pores. Here, we report on the compression of a filter cake by filtrating soft microgels in a microfluidic channel in front of a model membrane. To study the single colloid deformation amorphous and crystalline domains were built up in front of the membrane and visualized on-line using confocal fluorescence microscopy while adjusting the degree of permeation, i.e., the transmembrane flux. Results show locally pronounced asymmetric deformation in amorphous domains, while the microgels in colloidal crystals approached regular polyeder shape. Increasing the flux beyond the maximum colloid deformation results in non-isochoric microgel behavior. The presented methodology enables a realistic description of complex colloidal matter deposits during filtration.