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Different fungal species belonging to the <i>Colletotrichum</i> genus cause anthracnose disease in a range of major crops, resulting in huge economic losses worldwide. Typical symptoms include dark, sunken lesions on leaves, stems, or fruits. <i>Colletotrichum</i> spp. have synthesized, in vitro, a number of biologically active and structurally unusual metabolites that are involved in their host’s infection process. In this study, we applied a one strain many compounds (OSMAC) approach, integrated with targeted and non-targeted metabolomics profiling, to shed light on the secondary phytotoxic metabolite panels produced by pathogenic isolates of <i>Colletotrichum truncatum</i> and <i>Colletotrichum trifolii</i>. The phytotoxicity of the fungal crude extracts was also assessed on their primary hosts and related legumes, and the results correlated with the metabolite profile that arose from the different cultural conditions. To the best of our knowledge, this is the first time that the OSMAC strategy integrated with metabolomics approaches has been applied to <i>Colletotrichum</i> species involved in legume diseases.