Pomegranate peel flour was employed as a co-encapsulant of two lactic acid bacteria, by alginate emulsion templated microencapsulation, to enhance their resistance to thermal treatment, acidic pHs, and gastric conditions. Samples with pomegranate peel flour increased the tolerance to heat treatment, results consistent with thermal properties related to higher denaturation enthalpy of microcapsules. Co-encapsulated microcapsules also enhanced the survival to low pHs and enhanced almost 60% up the tolerance to bile salts. There was also an increase in survival rate against in vitro gastric acid conditions due to use of the co-encapsulant. In scanning electron microscopy, the incorporation of pomegranate peel flour resulted in a rough and porous structure, probably due to certain interference with the formation of spherical microcapsules, although it presented similar mean diameter, plus higher cell viability as confirmed by confocal laser microscopy. The obtained results indicate that co-encapsulation with a prebiotic ingredient represents a reinforcement of the physical microcapsule integrity to tolerate food process temperatures, besides retarding the adverse effect of acidic, bile salts, and simulated gastrointestinal conditions. The micro alginate co-encapsulation by ionic gelation with a prebiotic as pomegranate peel flour is a suitable alternative to develop thermal processed functional foods.