The objective of this study was to evaluate the effects of storage time and the use of different sugar types (crystal, refined, demerara, brown) on color characteristics, bioactive compounds, and antioxidant capacity of jaboticaba jellies. All analyses (microbiological, color, anthocyanins, vitamin C, total phenolic compounds, and antioxidant capacity by ABTS, DPPH, and β-carotene/linoleic acid systems) were performed for 120 days. The results were evaluated by means test and Pearson correlation. It was found that the sugars used in preparation and storage influenced the characteristics of jaboticaba jellies, and mold and yeast growth remained within the standards allowed by Brazilian legislation. All jellies were darkened during storage. Bioactive compound degradation was observed, and antioxidant capacity was reduced. Positive correlations were observed. Thus, demerara sugar, even though it does not provide bright colors in jellies, is the most beneficial for the production of jaboticaba jellies, due to the presence of nutritional compounds.