The microencapsulation of maqui juice by spray-drying and freeze-drying was studied as a strategy to protect anthocyanins in new food formulations in order to improve the anthocyanin retention before consumption and the bioaccessibility. It is well known that the encapsulation method affects both the shape and size of powders, being assumed that undefined forms of freeze-drying powders might affect their stability due to the high permeability to oxygen. The objective of this study was to compare the microencapsulation of maqui juice by spray-drying and freeze-drying, evaluating the stability of specific anthocyanins in yogurt and after in vitro digestion. Results indicated that most relevant differences between spray-drying and freeze-drying powders were the morphology and particle size that affect their solubility (70.4–59.5%) when they were reconstituted in water. Nevertheless these differences did not affect the stability of anthocyanins as other research have proposed. Both encapsulation methods generated powders with a high stability of 3-O-monoglycosylated anthocyanins in yogurt (half-life values of 75–69 days for delphinidin-3-sambubioside). Furthermore, no significant differences in the bioaccessibility of anthocyanins between maqui juice powders (44.1–43.8%) were found. In conclusion, the microencapsulation of maqui juice by freeze-drying is as effective as spray-drying to produce new value-added food formulations with stable anthocyanins.