The untargeted metabolomics analysis of polar and non-polar extracts from twenty-three Cannabis cultivars was carried out by two analytical platforms, GC–TOF/MS and LC–QTOF MS/MS, which allowed the identification of 169 compounds. Forty-six compounds were identified in polar extracts and 134 compounds in non-polar extracts, including cannabinoids, terpenoids, lipids and flavonoids, but also some interesting compounds such as amino and organic acids, among others. Although compositional differences were found in the profile of terpenoids and cannabinoids between extracts of plants cultivated in field and greenhouse, further studies must be accomplished including a greater number of cultivars to reach to a final conclusion. In this sense, the cultivation of a selected variety could be modified according to the production purposes.