This work describes a printing platform that utilizes components of two complementary techniques—microcontact printing and microfluidic patterning—to provide a high-throughput, reusable tool for patterning biomolecularly responsive chemical features on soft materials. Hydrogel substrates imprinted with biomolecular targets (e.g., proteins or peptides) are of considerable interest because of their utility in diverse bioanalytical applications such as diagnostics and studies of cells in culture. In the system described here, a track-etched polycarbonate membrane is used to seal a PDMS microfluidic channel device to form a print head. Model ‘inks’—solutions of biotin labeled biomolecular targets—are constantly replenished via perfusion of solution through the membrane and captured on a streptavidin-incorporating polyacrylamide hydrogel-coated substrate placed in conformal contact with the print head. The patterns obtained can be controlled through modifications of channel design and secondary programming via selective membrane wetting. Multiple channel designs have been used to pattern three model classes of biomolecular inks (i.e., peptides, polysaccharides, and proteins). Hydrogels patterned with polylysine are used to illustrate a specific biological application for this soft-patterning method, in this case directing in vitro primary mammalian hippocampal neuronal growth. The short cycle time and reproducibility of this soft-patterning technique are highlighted.