The demand for functional foods is increasing each year because consumers are gaining awareness about the importance of a healthy diet in the proper functioning of the body. Probiotics are among the most commonly known, commercialized, and studied foods. However, the loss of viability of probiotic products is observed during their formulation, processing, and storage. This study aimed to investigate the co-encapsulation of two Lactobacillus paracasei probiotic strains (LBC81 and ELBAL) with fructooligosaccharides (FOS) in a calcium alginate matrix using extrusion technology with gelatin as a coating material. The viability of the strains under gastrointestinal conditions and in storage at low temperature was also assessed. An immobilization yield of more than 59% was observed for both bacterial strains. Exposure to 2% biliary salts led to a decrease in the viability of free cells in the two L. paracasei strains, whereas the viability of microencapsulated cells increased up to 47%. After 35 days of storage at 4°C, the population of free cells was reduced, but microencapsulated cells remained stable after storage at low temperature. LBC81 bacteria microencapsulated with 1.5% FOS coated with gelatin were the most resistant to the stressful environments tested. Therefore, these results showed that co-encapsulation with FOS in a calcium alginate matrix coated with gelatin improved L. paracasei survival and may be useful for the development of more resistant probiotics and new functional foods.