This study shows an evaluation of the method to improve acid tolerance of probiotic bacteria aimed at enhancement of the probiotic effects in the intestinal canal. In the tolerance test of simulated digestive juice in vitro, the viable rate of Lactobacillus brevis subsp. coagulans (Labre) processed with chocolate (Labre-in-chocolate) is significantly increased, approximately one hundred times higher, compared to those of freeze-dried Labre powder and Labre contained in beverage. This protective effect depends on the content of water in chocolate for the probiotics processing. Differences in tolerance of metabolic activity were investigated with Labre-in-chocolate and freeze-dried Labre powder, both treated with simulated digestive juice in vitro. The enzyme activity of Labre-in-chocolate remained significantly even though that of the freeze-dried Labre powder was inactivated. These results indicate that chocolate processing is an effective method making probiotics to be delivered to the intestine in a viable condition and to be effective for host health.