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Conventional strategies for biological sensing require complex workflows to capture, isolate, and prepare biomolecules for specific and high-sensitivity detection. Instruments that facilitate these processes are usually cumbersome, reducing user-friendliness and accessibility. Here, we present a multichannel acoustic separator with biospecific and acoustically responsive microparticles to simplify workflows and shorten the time needed to isolate and detect biomarkers from complex fluids. The multichannel acoustic separator is 3D-printed and supports 12 acoustofluidic trapping channels that isolate the biospecific particles from off-target contaminants in the fluid. Fluid flow through the channels is driven by a semi-continuous siphon, which eliminates the need for fluid pumps. We tested the system for purifying three disparate biomolecules in individual and multiplexed formats, as well as the purification of IgA from whole blood for detection in approximately 70 min.