This article describes a method to isolate low concentration bacteria (10 - 103 CFU/mL) from large volumes of blood (typically of the order of 5 mL). Segmented microfluidics has been used for sequestering bacteria from blood using commercially available protein coated magnetic beads. Separation efficiencies of ~ > 90 % were obtained using the microfluidic method whereas the optimized traditional batch based protocol provided between 60 to 85% separation efficiencies. This is attributed to the good mixing efficiencies within the segmented microfluidic liquid slugs which are responsible for the rapid attachment of bacteria to the magnetic beads. © 2019 CBMS-0001.