A massive amount of fruit peels generated from fruit processing industries and household kitchens has resulted in nutritional loss and environmental problems. Pectin is a polysaccharide that is isolated from fruit peels and has been attributed to various applications. By proper waste management practices and the use of efficient methods for retrieval of pectin from fruit, peels would benefit from resource management. This study has aimed at the extraction of pectin from locally available fruit peels. Pectin extraction from banana–papaya peel was done by microwave‐assisted extraction. The influence of temperature, time, and pH on extraction yield and anhydrouronic acid content was analyzed using software Design Expert 11. The optimum operating conditions such as temperature, time, and pH to achieve maximum yield (23.74%) and anhydrouronic acid (69.97%) were determined as 73°C, pH 2, and 35 min, respectively. Physicochemical assets of the extracted pectin, such as moisture, ash, protein, methoxyl content, degree of esterification, equivalent weight, and acetyl value, were determined as 7.2 ± 0.27%, 6.20 ± 1.26%, 3.92 ± 0.05% 8.37 ± 0.42%, 67.91 ± 0.33%, 783.69 ± 0.46 g/mol, and 0.48 ± 0.11%, respectively, and some functional properties like water absorption capacity, oil absorption capacity, swelling capacity, and emulsifying activity and emulsion stability are found as 8.23%, 18.44%, 22.73%, 45.16%, and 29.33%, respectively.