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<i>Akkermansia muciniphila</i> is considered a next-generation probiotic to be incorporated in new food and pharmaceutical formulations. Effective delivery systems are required to ensure high probiotic viability and stability during product manufacture, shelf-life, and post-consumption, namely, throughout digestion. Hydrogelated matrices have demonstrated promising potential in this dominion. Hence, this work aimed to evaluate the effect of a calcium-alginate hydrogelated matrix on <i>A. muciniphila</i> viability during 28-days refrigerated aerobic storage and when exposed to simulated gastrointestinal conditions, in comparison with that of free cells. <i>Akkermansia muciniphila</i> was successfully encapsulated in the calcium-alginate matrix via extrusion (60% encapsulation yield). Furthermore, encapsulated <i>A. muciniphila</i> exhibited high stability (a loss in viability lower than 0.2 log-cycle) after 28-days of refrigerated aerobic storage, maintaining its viability around 10⁸ CFU/g. Prominently, as the storage time increased, encapsulated <i>A. muciniphila</i> revealed higher viability and stability regarding in vitro gastrointestinal conditions than free cells. This suggests that this encapsulation method may attenuate the detrimental effects of prolonged aerobic storage with a subsequent gastrointestinal passage. In conclusion, encapsulation via extrusion using a calcium-alginate hydrogelated matrix seems to be a promising and adequate strategy for safeguarding <i>A. muciniphila</i> from adverse conditions encountered during refrigerated aerobic storage and when exposed to the gastrointestinal passage.