The next-generation probiotics (NGPs) exhibit great therapeutic potential. However, some of these are found extremely oxygen-sensitive (EOS), leading to various challenges for their production, processing, storage, and colonic delivery. Sodium alginate (SA) appears as a promising encapsulating material for EOS probiotics thanks to its excellent oxygen barrier properties as well as optimal release behavior in simulated gastrointestinal fluid (SGF). This work comprehensively examines the effects of SA structural characteristics, molecular weight (MW), and Mannuronic/Guluronic (M/G) ratio on its functional properties as an encapsulating material for the protection and controlled release of 3 NGP strains, including Lactiplantibacillus plantarum, Bifidobacterium longum subsp. infantis and Faecalibacterium duncaniae (EOS strain). The results show that the rheological properties of SA are notably influenced by MW but not by the M/G ratio. Autoclaving SA powder significantly reduces the viscosity of SA solution. Although cross-linking with divalent cations slightly increases oxygen permeance, this still provides effective protection against oxygen for encapsulated microorganisms. SA beads with high MW and low M/G ratio form stronger gels due to effective G block crosslinking, while a high M/G ratio promotes bead swelling in SGF. The low MW SA beads dissolve in SGF after 4 h, especially the one with high M/G ratio which appears as ideal for swelling, solubility, and probiotic release. Even though pure SA does not protect enough probiotics in SGF, adding sodium carbonate and L-cysteine to the polymer matrix preserves F. duncaniae viability up to 6 logs CFU∙mL−1 after exposure to SGF.