The influence of the surface properties of chemically modified silicon nitride microsieves on the filtration of protein solutions and defatted milk is described in this research. Prior to membrane filtrations, an antifouling polymer based on poly(ethylene glycol), poly(TMSMA-r-PEGMA) was synthesized and applied on silicon-based surfaces like silicon, silicon nitride, and glass. The ability of such coating to repel proteins like bovine serum albumin (BSA) was confirmed by ellipsometry and confocal fluorescence microscopy. In BSA and skimmed milk filtrations no differences could be seen between unmodified and PEG-coated membranes (decreasing permeability in time). On the other hand, reduced fouling was observed with PEG-modified microsieves in combination with backpulsing and air sparging.