This study aimed to characterize and microencapsulate soybean seed coats phenolic compounds by spray‐drying, evaluating physicochemical properties and storage stability. Different extraction methodologies were used to obtain crude extract (SCE), ethyl acetate fraction, water fraction, and bound phenolic extract. Extraction yield, total phenolic and flavonoid contents, and antioxidant capacity were determined. HPLC–electrospray ionization source‐MS/MS analysis was performed on SCE. Microencapsulation by spray‐drying of SCE incorporating 10%, 20%, and 30% maltodextrin (MD) was carried out. Drying yield (DY), encapsulation efficiency (EE), moisture, morphology and particle size, dry, and aqueous storage stability were evaluated on the microcapsules. SCE had 7.79 g/100 g polyphenolic compounds (mainly isoflavones and phenolic acids) with antioxidant activity. Purification process by solvent partitioning allowed an increase of phenolic content and antioxidant activity. Microcapsules with 30% MD exhibited the highest DY, EE, and stability. Microencapsulated polyphenolic compounds from soybean seed coats can be used as functional ingredients in food products.Practical ApplicationSoybean seed coat is a usually discarded agro‐industrial by‐product, which presents antioxidant compounds of interest to human health. These compounds are prone to oxidation due to their chemical structure; therefore, microencapsulation is a viable and reproducible solution to overcome stability‐related limitations. Microencapsulation of soybean seed coats polyphenols is an alternative which protects and extends the stability of phenolic compounds that could be potentially incorporated into food products as a natural additive with antioxidant properties.