Though there are several commercial chromatographic systems for protein purification, development of cost-effective 3H-grade (high activity, high purity, and high activity) purification approaches is highly demanded. Here, we establish a methodology for encapsulating the IM7-displaying yeast cells in calcium alginate beads. Taking advantage of the biomaterial-based affinity chromatography, cost-effective purification of proteins with over 90% purity in a single-step is achieved. Moreover, our system is applied to coat multienzyme complex, leading to reusable biomaterials for high-efficient biocatalysis. Taken together, the present method has great application potential not only in the laboratory but also in industry for production of protein products.