Conventional agriculture might cause several damages to the environment and potentially threaten food security. Alternatively, agroecological agriculture is engaging efforts from the academy, social movements of small farmers, and public policies to become a win-win solution to the conciliation of ecosystems balance and food systems. However, there is lack information about the implication of the agroecological practices in food properties. In the present study, foodomics approach was employed to investigate changes in the metabolism from the volatile terpenoid profile of mint (Mentha x gracillis Sole) from conventional, organic and permaculture (a type of agroecological agriculture system) farms using headspace solid-phase microextraction (HS-SPME) associated to gas chromatography coupled to mass spectrometry (GC-MS) and chemometric tools. The discrimination among the three types of mint was successfully achieved and demonstrated evidence of ecological interaction impact in the food metabolism. Agroecological mint presented more oxygenated monoterpenes (α-terpineol, camphor, carveol, cavyl acetate, dihydrocarveol, dihydrocarvyl acetate, and myrtenyl acetate), which are compounds with more intense flavor and biological activities, while organic and conventional mint presented more monoterpenoid hydrocarbons and sesquiterpenes (α-pinene, α-cedrene, β-gurjunene, β-selinene, γ-muurolene, γ-terpinene, caryophyllene, and limonene). Furthermore, the discrimination between organic and conventional mint was effectively performed, which demonstrated different terpenoid profiles though without implying benefits for one or another agriculture system.