The recovery of bioactive compounds is a promising approach for obtaining rich extracts from fruit by-products. This study investigated the influence of Natural Deep Eutectic Solvents (NADES) and Ultrasound-Assisted Extraction (UAE) on the phenolic content, antioxidant capacity, and in vitro antidiabetic activity of Psidium myrtoides by-product. Among eight NADES evaluated based on choline chloride, NADES ChCl:Gly (1:2) was selected for its efficiency in extracting total phenolic compounds (TPC) with high antioxidant capacity. The optimized conditions were 61 °C, a solid–liquid ratio of 100 mg 5 mL−1, and a 60-minute extraction time. ChCl:Gly exhibited superior TPC recovery (2.6-fold greater effectiveness) compared to the 60 % hydroethanolic solution. Twenty-six phenolic compounds were identified, including significant levels of catechin (336.48 mg g−1) and isoquercetin (26.09 mg g−1). Phenolic acids, such as p-anisic acid (5.47 mg g−1) and methoxyphenylacetic acid (0.23 mg g−1), were identified for the first time in the purple araçá by-product. The ChCl:Gly extract demonstrated the highest bioactivity, showcasing antioxidant and antidiabetic capacities. This study introduces an innovative and sustainable alternative for recovering phenolic compounds from fruit by-products, offering enhanced recovery efficiency and/or selectivity compared to organic solvents.