We determined the effects of continuous access to drinking of water with a vinegar-based multi-micronutrient (VMm) supplement containing rice and fruit vinegars, vitamins, organic acids and sugars during gestation, lactation, and early adulthood in rats. Pregnant rats were provided with reverse-osmosis water or VMm water from the start of pregnancy through the time of weaning. Weaned pups consumed the same drinking water for 3–12 additional weeks. We examined fecal metabolite and microbial profiles, and other physiological parameters. Body weights were less in rats that drank VMm water. Thirty fecal metabolites involved in amino acid and dipeptide metabolism were significantly altered in VMm-supplemented rats. Analysis of microbial 16S rRNA showed enrichment of bacteria in the family S24–7 in VMm-supplemented rats, and one in Ruminococcaceae in controls. Our data show that a VMm-containing beverage can alter growth, and gut metabolism and microbial community. Future work to correlate these parameters is warranted.