The present study is focused on the utilization of fruit and agro-industrial wastes for the production of yeast pectinases using response surface optimization techniques. Orange peel (OP), groundnut oil cake (GC), MnSO4 and incubation period (IP) were found as significant parameters for pectinase production. The central composite design of media optimization indicated that OP (5), GC (4), MnSO4 (0.08%, w/v) and IP (48 h) increased the pectinase production by 9-fold. Crude pectinase promoted the enzymatic peeling of oranges and processing of raw banana fibers. Topographical changes of enzyme treated orange and mango peels were studied using AFM which provides a new tool to unravel the role of pectin aggregation in the dissolution of middle lamella during enzymatic hydrolysis. Changes in the fingerprint regions of enzyme treated fruit substrates were observed along with the disappearance of the impurities such as waxes and pectin using FTIR spectral analysis. © 2016 Elsevier Ltd.