β-Conglycinin is the main allergen present in soybeans, and it is causing wide concern due to its notable allergenicity, heat, and digestive enzyme resistance. Screening for aptamers that both recognize β-conglycinin and inhibit the allergic reactions that it triggers is necessary. Conventional aptamer screening is labor-intensive, requires skilled personnel, and has limited reproducibility. To address these limitations, an automated device was developed to enhance the efficiency of aptamer selection in Capture-SELEX. The device achieves highly integrated, reproducible, and accurate contamination control. Using this device, a high-affinity and specific aptamer, β-5, was selected with a