Habanero pepper (Capsicum chinense Jacq. var. Jaguar) leaves are an underutilized by-product and a source of phenolic compounds. This study evaluates how natural deep eutectic solvents (NADES) formulation and processing conditions with ultrasound-assisted extraction (UAE) modulate selective phenolic recovery. A 2×3×2 factorial design evaluated the hydrogen bond acceptor (HBA) in NADES (choline chloride, ChCl; malic acid, MAc), UAE time (10 min, 20 min, 30 min), and leaf drying (freeze-drying, FzD; oven-drying, OvD). Total phenolic content (TPC, Folin–Ciocalteu), antioxidant capacity (Ax, DPPH methodology), and individual polyphenols (liquid chromatography) were determined. The highest TPC was obtained with ChCl from FzD leaves at 10 min UAE (36.18 ± 0.70 mg GAE/g dry leaf). Maximum Ax occurred for OvD leaves at 30 min and did not differ between HBAs (ChCl 86.43 ± 0.65%; MAc 86.95 ± 0.18%). UPLC-DAD confirmed selectivity, highlighting catechin (51.14 ± 1.07 mg/g; MA, FzD, 20 min), chlorogenic acid (16.05 ± 0.09 mg/g; MA, OvD, 10 min), and quercetin + luteolin (5.37 ± 0.05 mg/g; MA, FzD, 10 min). Modulation could be explained by HBA-dependent polarity and hydrogen-bonding that alters solvation of phenolic compounds, while UAE enhances mass transfer and cell disruption, and drying-dependent matrix structure affect phenolic stability and release. These results show the behavior between total and individual phenolic compounds and the Ax, which guides the evaluation of UAE/NADES conditions for the targeted extraction of phenolic compounds of interest in the pharmaceutical, food and cosmetic industries from the leaf of Capsicum chinense.