An increasing body of evidence indicates that immunodysregulation and subsequent chronic low-grade inflammation can promote the development of stress-related somatic and psychiatric pathologies, including inflammatory bowel disease (IBD) and posttraumatic stress disorder (PTSD). Thus, immunoregulatory approaches counterbalancing basal and/or stress-induced immune activation should have stress-protective potential. In support of this hypothesis, we recently demonstrated that repeated s.c. preimmunization with a heat-killed preparation of the immunoregulatory bacterium Mycobacterium vaccae (M. vaccae; National Collection of Type Culture (NCTC) 11659), protects mice against stress-induced general anxiety, spontaneous colitis, and aggravation of dextran sulfate sodium (DSS)-induced colitis in the chronic subordinate colony housing (CSC) paradigm, a validated model for PTSD in male mice. In the current study, we repeatedly administered M. vaccae via the non-invasive intranasal (i.n.; 0.1 mg/mouse/administration) route, prior to or during CSC exposure or single housed control (SHC) conditions, and assessed the effects on general and social anxiety, and on parameters related to the severity of DSS-induced colitis. While administration of M. vaccae prior to the onset of CSC exposure only had minor stress-protective effects, administration of M. vaccae during CSC completely prevented CSC-induced aggravation of DSS colitis. As CSC in the current experimental setting did not reliably increase general anxiety-related behavior, potential stress-protective effects of M.vaccae are difficult to interpret. Taken together, these data broaden the framework for developing bioimmunoregulatory approaches, based on the administration of microorganisms with anti-inflammatory and immunoregulatory properties, for the prevention of stress-related disorders.