Mature coconut water is considered a waste product in the process of obtaining copra. However, it is a material that still contains substances that can be beneficial to the human body. For the processing of this material, the application of emerging technologies such as microwaves could help to reduce quality losses. For this reason, the effect of conventional and microwave processing was assessed on the inactivation kinetics of peroxidase (POD) in mature coconut water. Samples in glass tubes were treated at three temperatures (60, 75, and 90 ° C) and 5–130 s of holding time. First-order and Weibull kinetic models were adjusted considering the complete time-temperature profiles. Weibull model was the one that best described the inactivation of the POD enzyme, having the highest fit and lowest RMSE in both heating processes. Microwave heating generated an inactivation of the POD enzyme significantly faster than conventional processing in mature coconut water.