This study investigated the effect of pretreatment of orange and plantain peels on the inactivation kinetics and thermodynamic properties of polygalacturonase (PG) produced by Aspergillus awamori CICC 2040. Orange and plantain peel powders were subjected to microwave-assisted NaOH pretreatment and used as substrates for PG production. Un-treated peels served as controls. The PG was purified using acetone precipitation and column chromatography, and the inactivation kinetics, temperature dependency, and thermodynamic properties of the crude and purified PGs were determined. Higher inactivation rate constant was obtained for crude PG produced using pretreated orange peel (CPOF) and plantain peel (CPPF) compared to PG produced using untreated orange peel (Uo) and plantain peel (Up). At all the temperatures considered, higher half-life and decimal reduction time were recorded for CPOF and CPPF compared to Uo and Up. The highest half-life (45.60 min) and decimal reduction time (151.49 min) were recorded for CPOF at 60 ?C. Lower half-life and decimal reduction time were obtained for purified PGs compared to the crude PG. Polygalacturonase produced from pretreated peels had lower activation energy than those produced from untreated ones. The higher activation energy was recorded for the PG produced using orange peel compared to the one from plantain peels. The enthalpy of CPOF and CPPF was slightly lower than Uo and Up. The pretreatment of the peels resulted in a reduction of Gibbs free energy (?G ) and entropy (?S) of crude and purified PG. Higher ?G and ?S were recorded for the purified PG compared to the crude PG. Negative entropy and enthalpy were recorded for all the PGs. The findings from this study showed that the kinetic and thermodynamic properties of PG, produced by Aspergillus awamori CICC 2040, were enhanced by the pretreatment of orange and plantain peels.