Objective: Formulations containing probiotics are promoted due to health benefits. During lyophilization and subsequent storage in the gastrointestinal tract, bacteria are exposed to stress conditions that can lead to impairment and loss of viability. Methods: The suitability of various excipients for enhancing the stability and functionality of Bifidobacterium longum subsp. infantis during storage as freeze-dried powder and through exposure to acid and bile was investigated. Cells were lyophilized in the presence of sucrose, trehalose, lactose, cellobiose and fructooligosaccharide (FOS) and stored at 4 °C or 25 °C. The effect of diverse protectants on the persistence after exposure to acid and bile environment was examined through determination of the colony forming units, the β-glucosidase and β-galactosidase activity and the membrane integrity changes. Results: Cells freeze-dried in the presence of cryoprotectants had comparable survivability during storage at 4 °C whereas the survival rate at 25 °C of cells protected by cellobiose and FOS was higher than for those protected with sucrose and trehalose. Furthermore, the respective excipients used as cryoprotectants enhanced the stability of cells exposed to simulated gastric and small intestinal medium. Stabilization may be achieved through different mechanism of action such as protecting the membrane integrity and as metabolizable substrates. Overall, prebiotic and thus metabolizable protectants including cellobiose and FOS were superior to other protectants used. Conclusion: In symbiotic formulas with B. infantis, these sugars might serve as prebiotics and stabilizers of this probiotic strain during lyophilization, storage and in gastrointestinal conditions simultaneously, potentially increasing its health-promoting effects.