The propolis has potential to be a natural food additive. However, its application is limited, because it is alcohol-soluble and has strong flavour. Microencapsulation may be an alternative for reducing these problems. The aim of this study was to encapsulate propolis extract by complex coacervation using isolated soy protein and pectin as encapsulant agents. The coacervation was studied as a function of pH (5.0, 4.5, 4.0 and 3.5) and the concentration of encapsulants and core (2.5 and 5.0 g/100 mL). Samples obtained at pH 4.0 in both concentrations were lyophilized and analyzed for hygroscopicity, encapsulation efficiency, particle size, morphology, thermal behavior, stability of phenolic and flavonoids during storage, as well as antioxidant and antimicrobial activities. It was possible to encapsulate propolis extract by complex coacervation and to obtain it in the form of powder, alcohol-free, stable, with antioxidant property, antimicrobial activity against Staphylococcus aureus and with the possibility of controlled release in foods.