The aim of this study was microencapsulated a nanoemulsión of cocoa liquor with whey protein by spray drying, and evaluate the effect of different inlet drying temperatures on the properties of microcapsules. The nanoemulsion showed a particle size of 202.13 nm, PdI of 0.424 and ζ-potential of -25.20 mV. The inlet drying temperature showed differences in physicochemical properties of microcapsules. Microcapsules presented good thermal stability and protection against the melting of cocoa liquor. Microcapsules obtained showed excellent yields of polyphenolic compounds (78-93%), and high retention of volatile compounds, especially of pyrazines. Greater microencapsulation yield of bioactive compounds and retention of volatile compounds was obtained at higher drying temperature (180 °C). Excellent stability of polyphenols content, antioxidant capacity, and volatile compounds of cocoa liquor were observed during storage of the microcapsules at different temperature conditions, indicating the feasibility of this powder for its incorporation into functional foods.