Peel is a major bio-waste and a potential source of numerous bioactive molecules, creating immense environmental issues but no commercial significance. Thus, different extraction conditions, including chemical, enzymatic, ultrasonication, microwave, and homogenization, with varied sample concentrations at 2%, 5%, and 10% (w/v) were employed for maximum soluble dietary fiber (SDF) extraction from both mango (Totapuri and Safeda) and pomegranate (Bhagwa and Daru) peel. The maximum SDF yield of 29.26 ± 0.25% was observed at 5% w/v for homogenization-assisted enzymatic extraction (HEE) from mango peel (Safeda). The proximate and techno-functional properties of SDF exhibited efficient activity with enhanced thermal stability and structural characteristics. Scanning electron microscopy revealed a loosened and porous structure. In addition, the samples demonstrated significant prebiotic activity with the synthesis of three major short-chain fatty acids (SCFAs) in the order of propionic (3.60 ± 0.08 mg mL⁻¹) > acetic (2.64 ± 0.01 mg mL⁻¹) > butyric acid (1.27 ± 0.01 mg mL⁻¹), as quantified via ultra-performance liquid chromatography (UPLC). Thereby, this study highlights the role of waste fruit peel as a potent source of SDF, exhibiting profound prebiotic activity with imminent industrial application.