The present study demonstrates that the albedo (AP) and flavedo (FP) portions of Citrus maxima, are often discarded as agricultural waste that has the potential to manufacture high-quality pectin. The efficacy of green microwave aided extraction (MAE) technology for pectin extraction yield from both the portions of citrus peels was examined using a response surface technique. However, further advancement has to be made in improving the functional parameters required for MAE. The optimal conditions for increased pectin yields for albedo (YAP %) and flavedo (YFP %) were found to be solid to solvent ratio (1:15), time (95 s) and power (450 watt). The predicted values of YAP (5.35%) and YFP (3.13) were in accordance with experimental values of YAP (5.57 %) and YFP (3.09 %) with small error % i.e., 3.90 % and 1.29 % for AP and FP respectively. The AP and FP extracted at optimum conditions were compared with commercial pectin (Cp) based on physicochemical properties, color, FT-IR, FE-SEM/EDX, XRD, and particle size analysis. Experimental result shows that AP and FP were classified as high methoxy pectin due to high DE values 72.76 % and 74.98 % respectively.