The potential of passion fruit (Passiflora edulis Sims) epicarp to produce anthocyanin-based colorants with bioactive properties was evaluated. First, a five-level three-factor factorial design coupled with response surface methodology was implemented to optimize the extraction of anthocyanins from dark purple epicarps. The extraction yield and cyanidin-3-O-glucoside content were used as response criteria. The constructed models were fitted to the experimental data and used to calculate the optimal processing conditions (t = 38 min, T = 20 °C, S = 0% ethanol/water (v/v) acidified with citric acid to pH 3, and RS/L = 50 g/L) that lead to maximum responses (3.4 mg/g dried epicarp and 9 mg/g extract). Then, the antioxidant, antimicrobial, and cytotoxic activities of anthocyanin extracts obtained using the optimized method and a conventional extraction method were evaluated in vitro. The extract obtained by the optimized method revealed a higher bioactivity, in agreement with the higher cyanidin-3-O-glucoside content. This study highlighted the coloring and bioactive potential of a bio-based ingredient recycled from a bio-waste, which promotes a sustainable bioeconomy in the agri-food sector.