Food industries produce a high amount of waste every year. These wastes represent a source of bioactive compounds to be used to produce cosmetic and nutraceutical products. In this study, the possibility to retrain food waste as a potential source of bioactive metabolites is evaluated. In particular, metabolite profiles of different parts (bulb, leaves, stems and little stems) of fennel waste were investigated by liquid chromatography coupled with mass spectrometry (LC-ESI/LTQ Orbitrap MS). To discriminate the different plant parts, a Multivariate Data Analysis approach was developed. Metabolomic analysis allowed the identification of different metabolites mainly belonging to hydroxycinnamic acid derivatives, flavonoid glycosides, flavonoid aglycons, phenolic acids, iridoid derivatives and lignans. The identification of compounds was based on retention times, accurate mass measurements, MS/MS data, exploration on specific metabolites database and comparison with data reported in the literature for F. vulgare. Moreover, the presence of different oxylipins was relieved; these metabolites for the first time were identified in fennel. Most of the metabolites identified in F. vulgare possess anti-inflammatory, antioxidant and/or immunomodulatory properties. Considering that polyphenols are described to possess antioxidant activity, spectrophotometric tests were performed to evaluate the antioxidant activity of each part of the fennel.