The bioconjugation efficiency resulting from three PDMS based continuous flow micromixers are experimentally studied at various sample flow rates and pneumatic actuation frequencies. In this study, streptavidin-coupled paramagnetic microbeads and biotin-coupled fluorescent microbeads are separately injected into the micromixers and the resultant binding efficiency is measured by the fluorescence emission of the conjugated beads. The unconjugated beads are removed via magnetic separation. Fluorescence resulting from the conjugation process peaks at 10 Hz for each design. Fluorescence resulting from varying the sample flow rate indicates that bioconjugation efficiency peaks at specific flow rates, which vary slightly from design to design. The highest observed efficiency during flow rate tests was observed at 0.8 μL/min.