Chia seeds are a rich source of proteins and dietary fiber. Probiotics have been vastly studied as a functional food for our gut microbiome, improving the host’s immunity. Although their individualistic characteristics and benefits have been studied, but this particular combination hasn’t been looked into. Hence, this study will evaluate the effects of them administered in a combination against the individual and control groups on the intestinal barrier, brush border membrane functionality, inflammation biomarkers and the intestinal microbiota in-vivo (Gallus gallus). There are five groups, two control groups, non-injected (NI), and 18 MΩ water (H2O); and three experimental groups, 10 mg/ml (1%) hydrolyzed chia protein (CP), 10 mg/mL (1%) hydrolyzed chia seed protein + 106 CFU L. paracaesi (800 μL of hydrolyzed chia protein + 200 μL of probiotic/ egg) (CPP), and 106 CFU L. paracasei (P). The intra-amniotic administration of all the groups was conducted on day 17 of incubation. On day 21, the day fertile broiler eggs hatch, the chicks were euthanized to extract their cecum content, duodenum tissue and blood. Based on the heat maps and correlation analysis, the hydrolyzed chia protein group showed a decrease in the inflammation factor TNF-⍺ and Bifidobacterium; and upregulation of OCLN, MUC2, AP and Lactobacillus. The probiotic group showed upregulation of Lactobacillus and E.coli, whereas, a downregulation in Clostridium abundance and NF-𝜅β1. The overall morphology of the intestine showcased positive changes as observed in the treatment groups. However, the combination of both hydrolyzed chia protein and probiotic did not have a compound effect as expected. Further long-term studies are required to establish concrete relations in the intricate understanding of our intestinal health.