Abstract The probiotic activity in the intestinal microbiota depends on its survival during food storage and its passage through the gastrointestinal tract. This study aimed to evaluate the effect of storage and stress conditions such as temperature, pH and bile salts on the viability of Bifidobacterium animalis microencapsulated and incorporated in plantain flour. Between days 21 and 28, the failure percentage decreased from 93% to 27%. The mean counts of B. animalis were statistically different with change of temperature, pH and bile salt concentration. For the temperature, the counts obtained at 50 °C and 80 °C decreased by 60.1% and 90.2%, respectively. Likewise, at pH 2.5 showed a over 90% survival reduction during 60 min; whilst at pH 3.5 during 60 min the survivals were less than 50%. Finally, the counts achieved using 1 g/L of bile salts were higher than those obtained at 3 and 5 g/L. The results indicate the need to evaluate other capsular components to improve the survival of B. animalis microencapsulated and incorporated in plantain flour.