Berry fruits are well recognized for health-promoting constituents due to their properties of free radical scavengers which confer antioxidant activity against cellular oxidation reactions. Elderberry fruit contains one of the highest levels of anthocyanins. The objective of this work was to evaluate the storage stability of total monomeric anthocyanins, cyanidin-3-glucoside (one of two major anthocyanins in elderberry), and color parameters in freeze-dried elderberry encapsulated with a low proportion of different carriers (Maltodextrin, Capsul™, Promitor ™, and κ-carrageenan). Encapsulated samples were stored at two different water activities (aw) 0.10–0.20 and 0.43 at 38 ℃ for 90 days and evaluated for the content of monomeric anthocyanins, cyanidin-3-glucoside, color parameters, and physical characteristics. Freeze-dried powders remained free-flowing during storage at 38 ℃ with aw 0.12–0.20, but agglomeration occurred at aw = 0.43. Total anthocyanins and color parameter a* (redness) remained unchanged during storage at the lower aw. Glass transition temperatures (Tg) were determined and mostly correlated with observed physical phenomena. The powders had a very high total monomeric anthocyanin contents as high as 13 mg/g (cyanidin-3-glucoside). The addition of encapsulants in low proportions allowed the researchers to obtain elderberry powders with a very high concentration of total monomeric anthocyanins. aw plays a key role in all stability parameters studied.