For academic, biotech, and pharmaceutical scientists who are screening clones or performing high throughput protein purification, the goal is to automate the sample processing without sacrificing binding capacity. Traditionally, magnetic beads have facilitated process automation, but they lack the high binding capacity of agarose resins. On the other hand, agarose or sepharose resins have high binding capacity, but are not amenable to automation. Magnetic agarose resins combine the best of both formats by enabling high throughput sample processing with high protein binding capacity. Here we demonstrate the advantages of using magnetic agarose resins in simple benchtop protein purifications as well as their utility in 1) the screening of recombinant antibodies using the InvitrogenExpiCHOExpression Systems and 2) the purification of recombinant proteins expressed by in vitro translation (cell-free) systems using the Thermo Scientific KingFisherFlex magnetic particle processor. Both the Protein AG and anti-DYKDDDDK magnetic agarose supports result in isolation of >0.5mg protein per sample at >90% purity.