The agronomic production systems may affect the levels of food metabolites. Metabolomics approaches have been applied as useful tools for the characterization of fruit metabolomes. In this study, metabolomics techniques were used to assess the differences in phytochemical composition between goldenberry samples produced by organic and conventional systems. To verify that the organic samples were free of pesticides, individual pesticides were analyzed.  Principal component analysis showed a clear separation of goldenberry samples from two different farming systems. Via targeted metabolomics assays, whereby carotenoids and ascorbic acid were analyzed, no statistical differences between both crops were found. Conversely, untargeted metabolomics allowed us to identify two withanolides and one fatty acyl glycoside as tentative metabolites that differentiate goldenberry fruits, with organic fruits having higher amounts of these compounds than conventional fruits. Hence, untargeted metabolomics technology could be a suitable tool to research differences of phytochemicals grown under different agricultural management practices, and to authenticate organic products.