Approximately 30% of global carrot (Daucus carota) production is discarded, illustrating a significant example of food loss and waste within the supply chain. Rather than being sent to landfills, where discarded carrots contribute to environmental issues such as greenhouse gas emissions and incur disposal costs, they could serve as valuable sources of high-value commercial metabolites. The present study employs metabolomic analysis to explore bioprospecting of discarded carrot biomass sourced from three Colombian locations, contributing to reduced food waste and supporting a circular economy approach. This study investigates the metabolomic profiles of different carrot types—cracked (R), deformed (D), pathologically damaged (P), and healthy controls (C)—from distinct locations: Marinilla, El Santuario, and Rionegro located in the department of Antioquia- Colombia. These locations, with their unique climatic conditions, influenced the metabolomic composition of the residual carrots. Notably, Nuciferine and Cryptotanshinone were more abundant in the Rionegro and El Santuario carrots. At the same time, 4’-Methoxyflavonol, N-Hexadecanoylpyrrolidine, Microcystin LW, and Feruloyltyramine were found in higher concentrations in carrots from Marinilla. Moreover, Marinilla exhibited more metabolic diversity than Rionegro and El Santuario. The study also discusses the bioprospecting potential of these metabolites in residual carrots, highlighting their possible applications as well as waste valorization.