In this work, it was evaluated the effect of microencapsulation using spray drying over natural colorants present in two varieties (red and purple) of prickly pear juice (Opuntia spp.), using three kinds of carrier agents (matrixes). The dried samples after microencapsulation retained a high total amount of the betalains and their antioxidant characteristics. However, some individual betalains were lost after microencapsulation. According to ANOVA results, matrix 3204 showed a more protective effect than matrix 4801 in both microencapsulated juices over color, individual betalains, and antioxidant capacity. Globally, the protective effect was better for purple juices than red juices no matter the matrix used. Principal Component Analysis (PCA) confirmed these results. Matrix 3204 resulted in the best carrier agent since it gave a less disperse PCA group for both color juices. The parameters that separated both PCA matrixes groups were L*, a*, b* and DPPH.