Deactivation of polyphenol oxidase (PPO) in natural products is essential for downstream processing of functional molecules used as food or food additives, particularly those served as antioxidants. In the present work, we identified two proteins with PPO activity from lowbush blueberry using ammonium sulphate precipitation and chromatography procedures. Deactivation of these proteins was studied using aqueous solutions of ethanol of different concentrations. The PPO activity was recovered after ethanol removal for the protein samples previously soaked in a low concentration ethanol solution. A complete and unrecoverable deactivation of the proteins was achieved using ethanol with concentration over 70% (v/v), as manifested by the significant changes in circular dichroism (CD) and fluorescence spectroscopy measurements. Based on these findings, we propose a new extraction process for blueberry anthocyanin, in which an ethanol shock, Le. soaking blueberry fruit in a 70% (v/v) ethanol solution for 1 h, is implemented before subsequent procedures. This new process increases the anthocyanin yield by 55% in comparison to that without the ethanol shock (C) 2020 The Chemical Industry and Engineering Society of China, and Chemical Industry Press Co., Ltd. All rights reserved.