Persimmon fruit (Diospyros kaki Thunb.) production suffers great losses (15–20%) due to the inefficient overripening process. In order to valorise this waste, a compositional characterization of different fruit stages of the residues was done, and immature fruit was selected due to its high pectin and very high polyphenol content. A 3-level full factorial design was carried out to study the effect of temperature (70–95 °C) and low pH (0.5–1.5), on yield, degree of esterification, carbohydrate constituents, phenolic content and antioxidant capacity of the extracted pectin, and a complete polyphenol profile (UPLC-MS/MS) was performed on selected extracts. All responses could be accurately adjusted to the models (R2 > 80; lack of fit). Pectin yield, phenolic compounds and antioxidant activity ranged from 1.4 to 4.5%, 53.3 ± 2.27 to 111.7 ± 9.74 mg GAE/g pectin and 0.29 ± 0.01 to 2.77 ± 0.04 TEAC (Trolox μmol/mg pectin), respectively. A strong pectin-polyphenol interaction was found, which significantly enhanced acid resistance of both the pectin and polyphenol constituents, with optimum yield and polyphenol content at pH 1 and 95 °C. These new pectin-based ingredients might have a great potential as functional foods or natural food ingredients enhancing the quality and shelf-life.