The present study is focused on the extraction and characterization of pectin from different parts of Aegle marmelos (bael) fruit such as pulp, shells, and seeds on the dry and wet basis. Moreover, the comparative analysis of the extracted pectin from different fruit parts was also performed by using various parameters. Physicochemical properties, antioxidant activity, functional group, and structural analysis were carried out on the extracted pectin. In the present study, the yield percentage of bael seed pectin was found to be higher as compared to bael pulp pectin and bael shell pectin. The equivalent weight, methoxyl content, total anhydrouronic acid content (AUA), and degree of esterification (on a dry basis) of bael pulp, shell, and seed pectin were found to be 1119.53 ± 14.58 g/mol, 1095.01 ± 13.94 g/mol, and 1071.54 ± 13.35 g/mol; 7.25 ± 0.10%, 6.77 ± 0.03% and 7.39 ± 0.07%; 56.9 ± 0.81%, 54.56 ± 0.35% and 58.43 ± 0.60%; 72.37 ± 0.03%, 70.53 ± 0.22% and 71.88 ± 0.05%, respectively. On the other hand, the moisture content and ash content of bael pulp, shell, and seed pectin were found to be 10.23 ± 0.57%, 8.33 ± 2.08% and 9.9 ± 0.99%, and 6.77 ± 0.5%, 6.99 ± 0.66%, and 6.55 ± 0.50%, respectively which were in the acceptance range of purity. The functional group of extracted pectin was determined by Fourier transform infrared (FTIR) spectral analysis and peaks within the fingerprint region suggested that the extracted polysaccharide was pectin. Extracted bael pulp pectin demonstrated higher antioxidant activity with IC50 21.16 ± 0.99 µg/mL as compared to bael seed pectin (34.67 ± 1.34 µg/mL) and bael shell pectin (52.38 ± 0.62 µg/mL). The total phenolic content of bael pulp pectin was also found to be the highest (46.83 ± 2.8 mgGAE/g) in comparison with bael seed pectin (35.16 ± 2.8 mg GAE/g) and bael shell pectin (23.5 ± 5 mg yield percentageGAE/g). According to these findings, the bael seed has the maximum pectin output and AUA concentration, followed by the bael pulp and shell. However, the antioxidant activity and phenolic content were found to be highest in bael pulp. As a result, it was established that bael pulp and seed were a more significant source of pectin than bael shell. Although, pectin yielded from all parts of underutilized bael fruit can be utilized as a functional ingredient in biomedical and nutraceutical compounds and categorized as high-methoxyl pectin. © The Author(s) under exclusive licence to Society for Plant Research 2023.