Phenolic compounds can act as a substrate for colonic resident microbiota. Once the metabolites are absorbed and distributed throughout the body, they can have diverse effects on the gut. The objective of this study was to evaluate the effects of the intra-amniotic administration of a chia phenolic extract on intestinal inflammation, intestinal barrier, brush border membrane functionality, intestinal microbiota, and morphology in vivo (Gallus gallus model). Cornish-cross fertile broiler eggs, at 17 days of embryonic incubation, were separated into groups as follows: non-injected (NI; this group did not receive an injection); 18 MΩ H2O (H2O; injected with ultrapure water), and 10 mg/mL (1%) chia phenolic extract (CPE; injected with phenolic extract diluted in ultrapure water). Immediately after hatch (21 days), chickens were euthanized and their small intestine, cecum, and cecum content were collected and analyzed. The chia phenolic extract reduced the tumor necrosis factor-alpha (TNF-α) and increased the sucrose isomaltase (SI) gene expression, reduced the Bifidobacterium and E. coli populations, reduced the Paneth cell diameter, increased depth crypt, and maintained villus height compared to the non-injected control group. Chia phenolic extract may be a promising beneficial compound for improving intestinal health, demonstrating positive changes in intestinal inflammation, functionality, microbiota, and morphology.