The citrus by-products pectin and polyphenols were obtained from Citrus x lantifolia residues. The use of acid type, solute-solvent ratio, temperature, and extraction time on pectin yield recovery was evaluated using a factorial design 34; pectin physicochemical characterization, polyphenol profile, and antioxidant activity were also determined. Results indicated a total polyphenol content of 3.92 ± 0.06 mg Galic Acid Equivalents (GAE)/g of citrus waste flour in dry basis (DB), with antioxidant activity of 74%. The presence of neohesperidin (0.96 ± 0.09 mg/g of citrus flour DB), hesperidin (0.27 ± 0.0 mg/g of citrus flour DB), and ellagic acid (0.18 ± 0.03 mg/g of citrus flour DB) as major polyphenols was observed. All of the factors evaluated in pectin recovery presented significant effects (p < 0.05), nevertheless the acid type and solute-solvent ratio showed the greatest effect. The highest yield of pectin recovery (36%) was obtained at 90 °C for 90 min, at a ratio of 1:80 (w/v) using citric acid. The evaluation of pectin used as a food ingredient in cookies elaboration, resulted in a reduction of 10% of fat material without significant texture differences (p < 0.05). The pectin extraction conditions and characterization from these residues allowed us to determine the future applications of these materials for use in several commercial applications.