Scope: Both plant and animal products provide protein for human demands. However, the effect of protein sources on the physiological responses and the composition and functions of the gut microbiota during the early stage of life have received little attention. Methods and results: In the present study, chicken protein and soy protein are fed to young weaning rats for 14 days based on the AIN-93G diet formulation. The growth performance is recorded, and the morphology of the small intestine is analyzed to estimate the absorptive capacity. Shotgun metagenomic sequencing is applied to analyze the cecal microbiota. The chicken protein-based diet (CHPD) enhances growth performance and absorptive capacity in young rats compared to the soy protein-based diet (SPD). The CHPD maintains higher levels of Lactobacillus species, associated with glutathione synthesis. Conclusion: The CHPD seems favorable for young growing rats in relation to growth performance and absorptive capacity, correlated with changes in the composition and functional potential of the gut microbiota.