Anaerobic commensal gut bacteria are among the most promising future treatments for many diseases. Because of their sensitivity to oxygen and to the harsh conditions of the gut, few studies on formulations that deliver bacteria in a viable and functional form to the intestine have been done. The aim of this study was to develop a reliable and easy-to-scale-up process meeting these requirements. The designed process consisted of mixing a freeze-dried bacterium, Faecalibacterium prausnitzii, with a melted hydrophobic matrix (Gelucire® 43/01) to encapsulate them into a solid lipid base after cooling. These formulations were compared with freeze-dried beads containing bacteria encapsulated by ionotropic gelation. This work demonstrates that both formulations improve the survival of bacteria in the stomach and distal jejunum buffers during a digestive exposure test. However, only lipid inclusion provided sufficient protection suitable for therapeutic application. Nevertheless, Gelucire® poorly stabilizes bacteria during storage, unlike the freeze-dried beads.