Presence of browning or black-spot in fresh foods can adversely affect consumer acceptance. Onion has been reported to exert inhibitory activity against browning reaction. This research aimed to uncover the mechanism and identify active compounds in onion responsible for PPO inhibitors based on metabolomic approach. Onion was fractioned using different solvents, i.e n-hexane; chloroform; ethyl acetate; water, respectively. As a result, ethyl acetate fraction (EAF) of the onion demonstrated the strongest inhibition to PPO in comparison with other fractions, i.e. n-hexane, chloroform, and water. The reversible inhibitory activity of PPO by EAF occurred with presence of L-DOPA as substrate through competitive inhibition and Cu chelation in the active side of the PPO. Based on 1H-NMR (X) score plot and PPO inhibition (Y) using OPLS, NMR signals revealed that active compounds accounting for inhibition of PPO included quercetin, kaempferol, cyanidin 3.4’-di-O-β-glucopyranoside, quercetin 4-O-β-D-glucopyranoside, cyanidin 7-O-(3”-O-glucosyl-6”-O-malonyl-β-glucopyrano-side)-4’-O-β-glucopyranoside, cyanidin 3-(6”-O-malonyl) laminaribioside’.