Jaboticaba fruit has been linked to potential health benefits for humans, owing to the presence of numerous minor phytochemical compounds, notably phenolic compounds. These phytochemicals undergo extensive biotransformation during fruit digestion and absorption. The bioactivity of dietary phenolic compounds is greatly influenced by their bioavailability, which refers to the amount of compounds that reach target tissues and organs where they elicit biological activity linked to beneficial or adverse effects. This chapter describes recent findings on the biotransformation, bioavailability, and toxicity of minor compounds in jaboticaba fruit focusing on anthocyanins, hydrolyzable tannins, phenolic acids, flavonols, and flavanols. Specifically, experimental findings on the bioaccessibility and bioavailability of phenolic compounds from jaboticaba fruit using in vitro digestion models, rodents, and human trials are discussed. The interplay between the gut microbiota and jaboticaba’s bioactive compounds is also highlighted, focusing on their relationship with the bioavailability and bioactivity of phenolic compounds. Although the bioactive compounds identified in jaboticaba elicit several beneficial health effects, some phenolic compounds may pose toxic or adverse effects to humans under certain conditions. Thus, safety issues related to the bioactive compounds of jaboticaba fruit, as demonstrated by the limited preclinical and clinical models, are highlighted.