Chocolate is appreciated worldwide for its flavor and antioxidant properties. This study aims to evaluate the viability of Lactiplantibacillus plantarum, Lacticaseibacillus casei, and Bacillus subtilis in milk and 70% cocoa chocolates during 90-days. Chocolates incorporated with free and microencapsulated strains were subjected to a gastrointestinal tract (GIT) in vitro passage simulation. Results indicate that survival depends on the strain used; B. subtilis presented the highest performance, with values above 8.0 log CFU/g. GIT simulation demonstrated strains survival during the passage through all the phases, with intestinal phase average values above 7.9 log CFU/g for B. subtilis and L. casei; a factor attributed to the protection provided by the chocolate matrix. Bioaccessibility to phenolics, flavonoids, and antioxidants was also higher in all samples simulated analysis, and 70% cocoa chocolates showed the highest concentrations. The chocolates showed high acceptance in the sensorial analysis. The maintenance of the viability of potential probiotic microorganisms in the food matrix, and the high content of antioxidant compounds, indicate the great potential of chocolate for the diversification of probiotic foods currently available in the market.