Lactobacillus casei loaded chitosan-Ca-alginate microparticles enriched with the prebiotic fructooligosaccharide were prepared using spray-drying method associated with the polymers complexation and cross-linking with calcium. The concentrations of the formulation factors of alginate, chitosan and CaCl2 were optimized using 23 full factorial design. Experiments showed that microparticles with favorable physicochemical properties and high probiotic viability during preparation and storage could be obtained when 40 mg/g sodium alginate, 5 mg/g chitosan and 50 mg/g CaCl2 is used. Stability of L. casei during microencapsulation was identified by FTIR spectroscopy. The viability of the probiotic in the optimal formulation of synbiotic microparticles remained above the therapeutic minimum during incubation of 24 hours in simulated gastrointestinal conditions (7.67±0.4 log cfu/g) as well as after 3 months of cold storage (8.1±0.6 log cfu/g). High viability of L. casei was maintained during 6 weeks of cold storage when carrot juice was enriched with encapsulated cells. The effective preservation of L. casei into synbiotic microparticles provided production of new non-dairy functional food as an alternative of the population who is at risk of lactose intolerance.