Recently, edible films were shown to be an effective strategy for the delivery of functional ingredients, such as probiotics and prebiotics. With that in mind, two soluble fibres (inulin and fructooligosaccharides) were selected as prebiotic elements, in whey protein isolate (WPI) and alginate (ALG) matrices plasticized with glycerol and used for the incorporation of Bifidobacterium animalis subsp. lactis BB-12. The results obtained showed that the viability of the B. animalis subsp. lactis BB-12 probiotic strain was maintained within the minimum threshold (106 CFU/g) necessary to act as a probiotic throughout 60 days of storage at 23 °C. The incorporation of prebiotic compounds improved B. animalis subsp. lactis BB-12 viability, with inulin showing the best performance, as it maintained the viability at 7.34 log CFU/g. The compositional characteristics (biopolymer type and prebiotics addition) of the film forming solutions had no significant impact upon the viability of the probiotic strain. The incorporation of probiotics and prebiotics did not modify the infrared spectra, revealing that the molecular structure of the films was not modified. The moisture content and water solubility decreased positively in WPI- and ALG-based films with the addition of prebiotics compounds. Overall, the results obtained in this work support the use of WPI films containing inulin as a good strategy to immobilize B. animalis subsp. lactis BB-12, with potential applications in the development of functional foods.