Federal University of Bahia (Project no: 11301), FAPESB, CNPq and CAPES.Piper species are commonly used by indigenous communities to treat several gastrointestinal diseases. In China, they are also used as an active ingredient in formulae to treat cancer. The objective of the study was to perform a large-scale metabolite profiling analysis to identify bioactive compounds in Piper anisum. Antioxidant capacity was assessed by the DPPH assay and total phenolics were assessed by Folin–Ciocalteu’s method. Antimicrobial activity was assessed against several Grampositive and Gram-negative bacteria, whereas cytotoxicity was assessed against tumor cell lines MCF-7, HCT116, HepG2 and HL-60, and non-tumor cell line MRC-5. The multiplatform metabolite profiling approach encompassed NMR, GC–MS and LC–MS analyses. P. anisum root extract showed the greatest antioxidant capacity and total phenolic content, followed by the stem and leaf extracts. P. anisum extracts showed a highly selective antimicrobial profile, being specifically active against C. albicans (MIC of 500 μg mL−1). Additionally, the root extract (50 μg mL−1) showed the highest cell inhibition percentages against tumor cell lines MCF-7 (59.5%), HCT116 (49.2%), and HepG2 (61.0%). Forty-eight metabolites were annotated by GC–MS and 27 by LC–MS. These included alkaloids, carbohydrates, fatty acids, hydrocarbons, organic acids, phenolic compounds, and terpenes. Taken together, these results showed that P. anisum root extract is a promising source of bioactive compounds.