Traditional pectin extraction methods involve strong acids, which are environmentally harmful. This study explores an innovative approach using Malonic Acid (MA)-based Deep Eutectic Solvents (DES) to extract pectin from Artocarpus integer Peel (AIPP), optimised through Response Surface Methodology (RSM). The extracted AIPP-A and AIPP-B from ChCl-MA and ChDHCit-MA DES, respectively, were characterised for yield, pH, solubility, Degree of Esterification (DE), Water and Oil Holding Capacity (WHC and OHC). The experimental values aligned with RSM model predictions, with low standard deviations: 0.7300 for ChCl-MA and 0.1531 for ChDHCit-MA. Optimal extraction conditions for AIPP-A were 3.27 % ChCl-MA, 1.28 h extraction time, 50.44 °C temperature, and a 1:40 g/mL solid-to-liquid ratio. For AIPP-B, the conditions were 4.95 % ChDHCit-MA, 2.04 h extraction time, 79.65 °C temperature, and a 1:50 g/mL solid-to-liquid ratio. ChCl-MA yielded 30.97 % AIPP, which was higher than that of ChDHCit-MA (27.99 %). Both AIPP demonstrated desirable properties such as low pH, high solubility, and significant DE. AIPP-A exhibited a greater DE (58.40 %) compared to AIPP-B (32.4 %) contributed to its lower WHC and higher OHC. In conclusion, RSM-based optimisation of AIPP extraction with DES is effective in producing pectin that is suitable for use as a gelling agent, preservative, and stabiliser in the food industry.