Given the critical role of mucosal surfaces in susceptibility to infection, it is imperative that effective mucosal responses are induced when developing efficacious vaccines and prevention strategies for infection. Modulating the microbiota in the gastrointestinal (GI) tract through the use of probiotics (PBio) is a safe and well-tolerated approach to enhance mucosal and overall health. We assessed the longitudinal impact of daily treatment with the VSL#3 probiotic on cellular and humoral immunity and inflammation in healthy macaques. PBio therapy resulted in significantly increased frequencies of B cells expressing IgA in the colon and lymph node (LN), likely due to significantly increased LN T follicular helper cell (Tfh) frequencies and LN follicles. Increased frequencies of IL-23+ antigen presenting cells (APCs) in the colon were found post-PBio treatment, which correlated with LN Tfh. Finally, VSL#3 significantly down-modulated the response of TLR2, TLR3, TLR4 and TLR9-expressing HEK293 cells to stimulation with Pam3CSK4, Poly(I:C), LPS and ODN2006, respectively. These data provide a mechanism for the beneficial impact of PBio on mucosal health and implicates the use of PBio therapy in the context of vaccination or preventative approaches to enhance protection from mucosal infection by improving immune defenses at the mucosal portal of entry.