The objective of the investigation was to evaluate the viability, physicochemical properties, and stability of freeze-dried Weissella cibaria microcapsules in gastric and intestinal juices. W. cibaria microcapsules obtained by integrated technologies of double emulsion and complex coacervation were lyophilized and evaluated during storage at temperatures (5, 15, and 25 °C) and time (1, 2, 3, 4, 5, and 6 months). Dependent variables were evaluated: water activity (aw), moisture (Xw), solubility, hygroscopicity, peroxide index (PI), viability and simulated in vitro gastrointestinal digestion (SGD). Capsules stored at 5 °C retained the highest viability at 180 days of storage (7.8 ± 0.1 Log10 CFU g−1), ensuring adequate physicochemical properties: aw (0.507 ± 0.003), Xw (3.4 ± 0.1 %), solubility (33.1 ± 1.3 %), hygroscopicity (1.2 ± 0.3 %), PI (3.8 ± 0.1 meqO2 kg−1). While, at 25 °C viability reached 6.5 ± 0.1 Log10 CFU g−1. In general, it is highlighted that at the 3 temperatures, the probiotic character of the W. cibaria microcapsules is maintained during the 6 months of storage, which guarantees the effectiveness of the encapsulation method.