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A major goal in the discovery of bioactive natural products is to rapidly identify active compound(s) and dereplicate known molecules from complex biological extracts. The conventional bioassay-guided fractionation process can be time consuming and often requires multi-step procedures. Herein, we apply a metabolomic strategy merging multivariate data analysis and multi-informative molecular maps to rapidly prioritize bioactive molecules directly from crude plant extracts. The strategy was applied to 59 extracts of three <i>Bacopa</i> species (<i>B. monnieri</i>, <i>B. caroliniana</i> and <i>B. floribunda</i>), which were profiled by UHPLC-HRMS² and screened for anti-lipid peroxidation activity. Using this approach, six lipid peroxidation inhibitors <b>1</b>&#8722;<b>6</b> of three <i>Bacopa</i> spp. were discovered, three of them being new compounds: monnieraside IV (<b>4</b>), monnieraside V (<b>5</b>) and monnieraside VI (<b>6</b>). The results demonstrate that this combined approach could efficiently guide the discovery of new bioactive natural products. Furthermore, the approach allowed to evidence that main semi-quantitative changes in composition linked to the anti-lipid peroxidation activity were also correlated to seasonal effects notably for <i>B. monnieri</i>.