Black corn (Zea mays L.) has a distinct dark color that is shown to be attributed to the high anthocyanin content in its skin and kernel. In this study, the effect of black corn soluble extract (BCSE) was evaluated using an in vivo model (Gallus gallus) through intra-amniotic administration, where four groups (n=6-10) were tested: (1) non-injected; (2) 18 MΩ H2O; (3) 5% (5mg/mL) BCSE; (4) 15% (15 mg/mL) BCSE. The result showed that BCSE has an anti-inflammatory effect on the intestinal environment, that downregulations of NF-B, TNF- and IL-6 were observed. BCSE also modulates the intestinal microbiota by increasing the relative abundance of E. coli and Clostridium phyla. BCSE upregulates SGLT1 expression and result in higher hepatic glycogen content. BCSE enhances intestinal barrier function by increasing the expression of AMPK and CDX2. Beneficial morphometric changes promoted by BCSE includes increases in goblet cell (GC) number in the crypt; GC size in villi; Paneth cell number in the crypt, and acidic GC number in both crypts and villi.