Plinia cauliflora (Mart.) Kausel, popularly known as jabuticaba, possesses bioactive compounds such as flavonoids, tannins, and phenolic acids, known for their antioxidant, antibacterial, wound healing, and cardioprotective effects. Therefore, this study aimed to standardize the P. cauliflora fruit peel extraction method, maximize phenolic constituents, and evaluate their antioxidative and antimicrobial effects. Various extraction methods, including vortex extraction with and without precipitation at 25, 40, and 80 °C, and infusion extraction with and without precipitation, were performed using a completely randomized design. Extraction without precipitation (E − P) showed the highest yield (57.9%). However, the precipitated extraction (E + P) method displayed a yield of 45.9%, higher levels of phenolic derivatives, and enhanced antioxidant capacity. Major compounds, such as D-psicose, D-glucose, and citric acid, were identified through gas chromatography–mass spectrometry (GC-MS) analysis. Ultra-high-performance liquid chromatography–tandem mass spectrometry (UHPLC-MS/MS) analysis identified citric acid, hexose, flavonoids, tannins, and quercetin as the major compounds in the extracts. Furthermore, the extracts exhibited inhibitory effects against Bacillus subtilis, Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli bacteria. In conclusion, the E + P method efficiently obtained extracts with high content of bioactive compounds showing antioxidant and antimicrobial capacities with potential application as a dietary supplement.