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The production of a large volume of agricultural residue during the processing of fruits has resulted in environmental problems. Therefore, the production of bioactive compounds from agricultural residue will provide a direction to overcome these issues. These residues are a potential source of many bioactive compounds, such as pectin. The present study deals with the extraction and characterization of pectin from the Bael pulp residue produced during the processing of Bael fruit. Pectin was extracted by using hot acid extraction methods and evaluated for its physicochemical properties by using Fourier transform infrared spectroscopy (FTIR), scanning electron microscope (SEM), X-ray diffractometer (XRD), and the values of moisture content, ash content, equivalent weight, methoxyl content, total anhydrouronic acid content, and degree of esterification. The results were compared with those of commercial pectin. Bael pulp residue yielded 24.02 ± 0.63% of pectin by using HCl and 22.1 ± 0.7% by using H2SO4. The physicochemical characterization of extracted pectin, such as equivalent weight (852.32 ± 8.43), methoxyl content (8.28 ± 0.35%), total anhydrouronic acid (67.69 ± 0.35%), and degree of esterification (69.39 ± 0.57%), was within the acceptable range and comparable with the commercial pectin. The values of moisture content (4.62 ± 1.14%) and ash content (5.22 ± 0.66%) indicated that the extracted pectin was in pure form. SEM and XRD patterns observed the rough and amorphous nature of extracted pectin. The antioxidant activity of pectin and total phenolic content were also observed. The IC50 value was found to be 15.74 µg/mL, showing an adequate amount of antioxidant activity in isolated pectin with a total phenolic content of 58.5 mg Gallic acid equivalent (GAE)/g. Additionally, the prebiotic potential of extracted pectin was confirmed by the viability assay of two probiotics (Bacillus clausii and Saccharomyces boulardii). Based on these results, Bael pulp residue could be a good alternative source of high-value pectin that could be used to make health products and other biological applications. [ABSTRACT FROM AUTHOR]