Abstract Borracheros or Angel Trumpets ( Brugmansia spp.) of the Solanaceae plant family are known for producing scopolamine and other tropane alkaloids and are widely used by indigenous communities in the Andes for medicinal and ritual purposes. Growing different varieties has increased the popularity of Brugmansia species in recent years, leading to the promotion of hybridization to get new morphotypes. However, so far no medical or cultural use of plant extracts could be linked to selected Brugmansia species or cultivars. Moreover, until now there is only limited knowledge about the effect of hybridization on tropane alkaloid contents and/or diversity of Brugmansia species or cultivars. Here, a liquid chromatography-mass spectrometry (LC-MS) approach was applied to identify and characterize secondary metabolite contents in various Brugmansia species and hybrids from different geographic origins in Colombia. The analysis of the metabolic data sets revealed that tropane alkaloids and other secondary metabolites accumulate in a leaf and flower specific manner. Although some minor differences were found between Brugmansia subgroups, the only significant difference exists between plants collected in the Sibundoy Valley, where they have been domesticated by indigenous communities since a long time and those, which so far have not been used by humans at all. The different genetic constitutions of Brugmancia species and cultivars are not the dominating reason for their differences in tropane alkaloid contents and medical and cultural usages, as there is no clear taxonomical signature based on the metabolite properties for species segregation. Instead, their use by indigenous communities during ceremonies and for medical treatment such as wound healing, infection control, rheumatism and arthritis is rather caused by the plasticity of the individual plants to react to the local abiotic and biotic environments by the variation of secondary metabolite composition and by the differences in the bioavailability of the active compounds as result of the extraction method.