The chitosan microcapsules containing Brazilian red propolis extract (RPE) obtained by spray-drying also called Chitosanates of Red Propolis Extract (ChRPE) were prepared and characterized using techniques of Particle Size, Scanning Electron Microscopy, Infrared Spectroscopy, Thermal Analysis, dissolution studies and antibacterial activity. The chitosanate hydrogels was prepared and particle size analysis showed sub-population of particles between 0.30 to 8.00 µm. The ChRPE in solid-state showed a rounded shape and particle diameter between 1.0 and 30 µm by SEM analysis. The thermal analysis and FTIR data demonstrate encapsulation of the bioactive red propolis extract into chitosan biopolymeric system and chemical reaction between chitosan and RPE was not detected. The ChRPE35, ChRPE50 and ChRPE75 demonstrated in vitro release of flavonoids following a concentration-dependent and pH-dependent model. The modified release in simulate gastrointestinal tract conditions was proved. The chitosanate microcapsules obtained in the solid-state were reversibly dissolved in chitosanate hydrogels in an appropriate dissolution medium to release the active flavonoids from the Brazilian red propolis extract. Antibacterial activity against Staphylococcus aureus was demonstrated in the ChRPE. The ChRPE can be easily incorporated into food, in the production of biodegradable films, as a bio-preservative and can be manufactured by the pharmaceutical and nutraceutical industries.