Antibiotics are effective treatments for bacterial infections, however, their oral administration can have unintended consequences and may alter the gut microbiota composition. In this study, we examined the influence of antibiotics on the induction of gut dysbiosis and then evaluated the potential of cow and goat milk to restore the microbiota composition and metabolism in newly weaned rats. In the first study (gut dysbiosis model), rats were treated with amoxicillin, a mixture of antibiotics (ampicillin, gentamicin and metronidazole) or no antibiotics (control). Antibiotics reduced the rat body weights, food intakes and faecal outputs compared to the control group. Gut length was significantly decreased after the antibiotic intake. The bacterial populations (Bifidobacterium spp., Lactobacillus spp. and total bacteria) and short-chain fatty acids (SCFAs; acetic, butyric and propionic) concentrations in rat caecum, colon and faeces were significantly altered by the antibiotic treatments. In the second study, we examined the effects of cow and goat milk in restoring bacterial populations and metabolism in rats with gut dysbiosis induced by amoxicillin. Goat milk significantly increased the numbers of Bifidobacterium spp. and Lactobacillus spp. and decreased the numbers of Clostridium perfringens in the caecum and colon of rats treated with amoxicillin. Whereas, rats fed cow milk had higher Lactobacillus spp. and lower C. perfringens in the gut. Caecal and colonic SCFAs (acetic, butyric and propionic) concentrations differed significantly between rats fed cow and goat milk diets. Overall, goat and cow milk varied in their effects on the immature gut following antibiotic-induced dysbiosis in a rat model.