The human intestinal system is a complex of various anaerobes including extremely oxygen-sensitive (EOS) bacteria, some of which have been credited with significant health benefits. Among these, Faecalibacterium prausnitzii, which is one of the most abundant anaerobic bacterial strains in the human intestinal tract, has been proved to be a promising probiotic for the treatment of inflammatory bowel diseases. However, because of its extremely sensitive nature, there are many difficulties when passing through the harsh environment of the gastrointestinal tract. Hence, in this study, a comprehensive physicochemical characterization was performed for the use of polysaccharides from several origins (hydroxypropyl methyl cellulose, methyl cellulose, hydroxypropyl cellulose, chitosan, low-methoxylated pectin, kappa-carrageenan, sodium alginate and pullulan) as encapsulating agents to protect and deliver this bacterium. First, the apparent viscosity and surface tension of the polymer solutions were tested. Then, the mechanical properties, water vapor and oxygen barrier properties of these biopolymers as self-standing films were investigated. Lastly, in vitro release profiles of small molecules and bacterial cells from these biopolymer matrices in contact with a simulated gastrointestinal tract were evaluated. The results showed that chitosan, low-methoxylated pectin, kappa-carrageenan, sodium alginate and pullulan films exhibited good oxygen barrier properties to protect EOS probiotics. Among all the biopolymers tested, sodium alginate exhibited the best oxygen barrier properties and release profile. The release kinetics can be modulated by several factors including biopolymer type, plasticizer concentration and active molecules or bacteria to be encapsulated. On that basis and integrating the other parameters analyzed, a multicriteria strategy for probiotic encapsulation was proposed.