This study evaluated the antioxidant and antibacterial potential of Passiflora edulis (passion fruit) at three ripening stages—intermediate, ripe, and overripe—to determine the optimal consumption time based on the presence of secondary metabolites (polyphenols, alkaloids, and anthocyanins). Fruits from Costa Rica, including pulp and peel, were analyzed. Qualitative assays (Dragendorff, Mayer, Lieberman Burchard, Ferric Chloride, and Shinoda) and quantitative analyses using Folin–Ciocalteu (total polyphenols), ORAC (antioxidant activity), and Kirby–Bauer (antibacterial activity) methods were conducted. Acetone–water (7:3) was the most effective solvent, with three extractions yielding optimal results. Peels contained significantly higher polyphenols (7.2 ± 0.1 mg GAE/g d.w.) and antioxidant activity (2403 ± 519 µmol TE/g d.w.) than pulps. Anthocyanins were abundant in both, while antibacterial activity was more effective in peels, inhibiting Gram-positive bacteria with 25% relative inhibition, but showing no activity against Gram-negative strains. These findings highlight passion fruit peel as a rich source of bioactive compounds with strong antioxidant and antibacterial properties, particularly in intermediate and overripe stages, supporting its potential use in the development of functional ingredients for nutraceutical applications and promoting sustainable waste management.