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A new flow-through method for rapid capture and detection of microorganisms is developed using optically-flat microengineered membranes. Selective and efficient capture of Salmonella is demonstrated with antibodies coated on membranes (microsieves) having a pore size much larger than the microorganism itself. The silicon-nitride membranes are first photochemically coated with 1,2-epoxy-9-decene yielding stable Si–C and N–C linkages. The resultant epoxide-terminated microsieves are subsequently biofunctionalized with anti-Salmonella antibodies. The capture efficiency of antibody-coated microsieves with different pore sizes (2.0–5.0 μm) is studied with Salmonella enterica enterica serotype Typhimurium suspensions (107 cfu mL–1). The antibody-coated microsieves capture 52% (2 μm microsieves), 30% (3.5 μm microsieves), and 12% (5 μm microsieves) of Salmonella from the suspension. The influence of flow rate (0.8–16 μL min–1 mm–2) on the capture efficiency of antibody-coated 3.5 μm microsieves is investigated. The capture efficiency increases from ≈30% to ≈70% when the flow-rate decreases from 16 to 0.8 μL min–1 mm–2. Antibody-coated 3.5 μm microsieves can capture Salmonella rapidly and directly from fresh milk suspension (capture 35% at concentration of 80 cfu mL–1). The use of antibody-coated microsieves as microbial selective capture devices is thus shown to be highly promising for the direct capture of microorganisms.