Green coconut water has unique nutritional and sensorial qualities. Despite the different processing technologies studied, its enzymatic stability is still challenging. Peroxidase (POD) is known to be a resistant enzyme, responsible for undesirable effects on coconut water, as the development of pinkish and/or dark brown colour. This study evaluated the use of ultrasound technology (US) for inactivation and thermal sensitization of coconut water peroxidase (POD). The effects of US application alone and as a pre-treatment to thermal processing were evaluated. The enzyme activity was reduced in only 27% after 30 min of US processing (286 W/L, 20 kHz), demonstrating its high resistance. Furthermore, US technology showed a positive impact on subsequent thermal processing. The enzyme thermal inactivation kinetics showed non-linear behaviour, which was modelled according to the Weibull distribution function under non-isothermal conditions. The enzyme became sensitized to heat after US pre-treatment. The coconut water POD with US pre-treatment showed lower thermal resistance than the native one, probably due to structural changes that caused the enzyme population to be more homogeneous. Therefore, its resistance distribution became more uniform, allowing lower processing time and/or temperature. The results suggest that US is a good technology for sensitizing enzymes allowing the use of milder thermal processing.