The viability of probiotics is affected by several factors during manufacturing, storage and gastrointestinal tract passage. Protecting the probiotics from harmful conditions is particularly critical for oxygen sensitive species like Akkermansia muciniphila, a bacterium which recently has been proposed as a next-generation probiotic candidate. Previously, we have developed a protocol for microencapsulating A. muciniphila in a xanthan/gellan gum matrix. Here, we report the enhanced survival during storage and in vitro gastric passage of microencapsulated A. muciniphila embedded in dark chocolate. Lactobacillus casei, as a representative species of traditional probiotics, was included in order to compare its behavior with that of A. muciniphila. For A. muciniphila we observed a 0.63 and 0.87 log CFU g-1 reduction during 60 days storage at 4°C or 15°C, respectively. The viability of L. casei remained stable during the same period. During simulated gastric transit (pH 3), microencapsulated A. muciniphila embedded in chocolate showed 1.80 log CFU mL-1 better survival than naked cells, while for L. casei survival was improved with 0.8 log CFU mL-1. In a hedonic sensory test, dark chocolate containing microcapsules were not significantly different from two commercially available chocolates. The developed protocol constitutes a promising approach for A. muciniphila dosage.