Bidens pilosa L. (fam. Asteraceae) is an annual herb used globally in phytotherapy and each plant material or the whole plant have been declared to be effective. Therefore, the aim of the present study was to conduct metabolomic profiling of different plant materials, including the quali-quantitative composition of phenolic compounds. The intrinsic scavenging/reducing properties and antimicrobial effects of the extracts were assayed against numerous bacterial, Candida and dermatophytes species, whereas docking runs were conducted for tentatively unravelling the mechanism of action underlying antimicrobial effects. Oligosaccharide, disaccharide and fatty acids were present at higher concentrations in root rather than in the other plant parts. Monoglycerides were more abundant in stem than in the other plant parts, whereas peptide and diterpenoid were prominent in leaf and root, respectively. By contrast, amino acids showed very different distribution patterns in the four plant parts. Regarding the phenolic composition, appreciable levels of caftaric acid were found in most of the analyzed methanol extracts, that were also particularly efficacious as antiradical and anti-mycotic agents against C. albicans and dermatophytes. The docking experiments also showed a micromolar affinity of caftaric acid towards the lanosterol 14α-demethylase, deeply involved in fungal metabolism. In conclusion, the present study corroborates the B. pilosa as a phytotherapy remedy against infectious disease.