Previous studies have assessed the properties of aqueous extracts, using byproducts such as jaboticaba peel. We have assessed potential antioxidant effects of jaboticaba extract (Plinia jaboticaba) (JAE = 50 g/L) in vitro and in vivo. Healthy Wistar rats received ad libitum JAE for either 15 or 49 days in vivo. Cyanidin-3-O-glucoside, delphinidin-3-O-glucoside, gallic acid, rutin, myricetin, and quercetin were identified as the main polyphenols in JAE. Lipid peroxidation values in the serum and colon were similar throughout the groups. In addition, JAE did not disturb the antioxidant systems. JAE also altered gut microbiota, increasing since Lactobacillus, Bifidobacterium and Enterobacteriaceae counts. Bacterial metabolites were higher in the colon content of rats fed with JAE than in the control group. Given these results, under healthy conditions, JAE dietary supplementation could perform in vivo modulation of gut microbiota, without disturbing the antioxidant system. PRACTICAL APPLICATION: Jaboticaba (Plinia jaboticaba) peel is a rich and often-wasted source of bioactive compounds, such as polyphenols. Previous studies have shown that physiological benefits of this berry. The jaboticaba peel could contribute to antioxidant defense systems; it may also have an effect over gut microbiota related to polyphenols contents. Aqueous extraction may be a practical way of employing the bioactive compounds of jaboticaba peel; these compounds can be consumed daily and safely, and thus have attracted particular attention. This work showed positive impacts of jaboticaba peel treatments on microbiota and antioxidant defense systems, and could guide future clinical studies.