Propionibacterium freudenreichii is an emergent probiotic, presenting several beneficial effects including anti-inflammatory properties, mediated by surface layer proteins (SLPs) belonged to the S-layer lattice, in particularly the protein SlpB. We hypothesize cheese matrix may be the best delivery vehicle for P. freudenreichii’s anti-inflammatory potential, by enhancing propionibacteria survival to digestives stresses, and by allowing undamaged SLPs to reach the digestive tract. Firstly, we compared the immunomodulatory effects of P. freudenreichii and intact SLPs, to SLPs digested by trypsin, i.e SLPs-peptides on HT29-cells. In contrast to P. freudenreichii and SLPs, SLPs peptides don’t reduce pro-inflammatory cytokines expression during cells co-stimulation with lipopolysaccharide. This result confirmed the importance to protect SLPs from proteolysis to permit them to trigger gut immune system. Secondly, we evaluated propionibacteria resistance and slpB proteolysis during in vitro static digestion, in different delivery vehicles increasingly concentrated in dairy proteins: milk ultrafiltrate, milk and cheese. The experiment clearly showed the protective effect of the Slp proteins by the cheese matrix and better bacterial viability. Then, we carried out in vitro a dynamic digestion using Didgi® system. We selected two matrices only: the milk ultrafiltrate and the cheese. We decided to apply fixed digestion parameters for both matrices: the digestive parameters of cheese. The results show a protective effect of the cheese matrix on the viability of the propionic bacteria and on SLPs against digestive proteolysis. Taken together, those results show that cheese is an adequate delivery vehicle for P. freudenreichii immunomodulatory proteins.