Bile acids (BA) have recently emerged as regulators of intestinal immune homeostasis and mucosal integrity. We examined the effects of administering enterally deoxycholic acid (DCA) to early-weaned pigs challenged with lipopolysaccharide (LPS) on gut BA profile, immune response and microbiota. Twenty-four piglets were weaned at 21 d, acclimatized for 14 d, and subsequently grouped (n = 8) to be intragastrically infused with either deionized water (C+, C−) or 15 mg of DCA·kg⁻¹ initial BW (DCA) daily during 14 d. On d 28, C+ and DCA piglets were injected i.p. with 150 µg LPS·kg⁻¹ BW. Three h later, all animals were bled and killed for organ measurement and sampling. Blood samples were analyzed for endotoxin (EDT), interleukin (IL)-6, and tumor necrosis factor α (TNF-α). Expression of occludin, IL-6 and IL-10 genes and the concentration of individual BA were measured in the ileal mucosa. Colonic microbiota was characterized by sequencing bacterial 16S ribosomal-RNA. Individual BW and feed intake were recorded weekly. Data were analyzed with a mixed-effects model in which pig was treated as random effect and treatment as fixed effect. Compared with C-, LPS decreased total BA concentration (P < 0.01) and increased plasma TNF-α (P < 0.01) and EDT (P < 0.02) as well as hepatic (P < 0.01) and intestinal (P < 0.03) weight. Interestingly, DCA infusion increased the proportion of BA with the greatest ability to induce BA-signaling pathways (P < 0.05), prevented alterations (P > 0.10) in plasma EDT and intestinal weight, decreased expression of IL genes (P < 0.04) in the ileum, and enhanced (P < 0.05) feed intake. In addition, treating pigs with DCA increased (P < 0.05) Peptostreptococcaceae and Clostridiaceae whereas decreased (P < 0.05) Lactobacillaceae in the colon. In conclusion, DCA acted locally to prevent LPS-induced inflammation and barrier disruption of the intestinal mucosa. These effects were associated with changes in the intestinal BA signature.