Abstract Jaboticaba (Plinia cauliflora) is a Brazilian native fruit which can be consumed in natura form, and also as processed food. The skin has a significant biological nutritional potential. The present study aimed to evaluate the bioactive compounds of the jaboticaba skin and of the jaboticaba skin flour (JSF), and its application in cookie. Physicochemical analyses to determine the bioactive compounds and antioxidant activity (TEAC and FRAP) of jaboticaba skin and JSF were performed. Skin presented high content of phenolic compounds, anthocyanins, flavonoids and condensed tannins, strengthening that this composition exhibited considerable levels of antioxidant activity. The JSF presented considerable carbohydrate contents, phenolic compounds and antioxidant activity, besides being a source of fibers. The cookies were prepared by replacing 2.5%, 5.0% and 7.5% of the total amount of whole wheat flour in the recipe by JSF. The formulations presented positive increases of bioactive compounds, contributing with the potential of antioxidant activity. All formulations were well accepted in the sensory evaluation.