Filter cake formation is the predominant phenomenon limiting the filtration performance of membrane separation processes. However, the filter cake’s behavior at the particle scale, which determines its overall cake behavior, has only recently come into the focus of scientists, leaving open questions about its formation and filtration behavior. The present study contributes to the fundamental understanding of soft filter cakes by analyzing the influence of the porous membrane’s morphology on crystal formation and the compaction behavior of soft filter cakes under filtration conditions. Microfluidic chips with nanolithographic imprinted filter templates were used to trigger the formation of crystalline colloidal filter cakes formed by soft microgels. The soft filter cakes were observed via confocal laser scanning microscopy (CLSM) under dead-end filtration conditions. Colloidal crystal formation in the cake, as well as their compaction behavior, were analyzed by optical visualization and pressure data. For the first time, we show that exposing the soft cake to a crystalline filter template promotes the formation of colloidal crystallites and that soft cakes experience gradient compression during filtration.