Purple flesh cultivated potato (PP) is a foodstuff scarcely cultivated in the world but with high potential because of its anthocyanin content. Moreover, it has been little explored as a source of anthocyanins (AT) for further applications in formulated food products. The main goal of this research was to study the effect of maltodextrin (MD) and spray drying conditions on the encapsulation efficiency (EE) and bioaccesibility of AT from purple flesh cultivated potato extract (PPE). The anthocyanin-rich extract was obtained from PP and microencapsulated by spray-drying, using MD as the encapsulating agent. A statistical optimization approach was used to obtain optimal microencapsulation conditions. The PPE microparticles obtained under optimal conditions showed 86% of EE. The protector effect of microencapsulation on AT was observed to be stable during storage and in vitro digestion. The AT degradation rate constant was significantly lower for the PPE-MD than for the PPE. The assessed bioaccesibility of AT from the PPE-MD was 20% higher than that of the PPE, which could be explained by the protective effect of encapsulation against environmental conditions. In conclusion, microencapsulation is an effective strategy to protect AT from PP, suggesting that AT may be an alternative as a stable colorant for use in the food industry.