Ayahuasca is a brew prepared from the water decoction of two Amazonian plants, which is legally used for religious, cultural or therapeutic activities. The potential use of ayahuasca as a natural or phytotherapeutic drug is directly linked to the action of its active compounds and their connection with the therapeutic efficacy of the beverage. In this context, the aim of the present study was to establish a selective, sensitive and reproducible analytical method for the quantification of the main active ayahuasca compounds. Thirty-eight samples from the state of São Paulo, Brazil, were analyzed and the simultaneous quantifications of N,N-dimethyltryptamine (DMT), tetrahydroharmine (THH), harmine (HME) and harmaline (HML) were performed. This study enabled the development of a fast validated analytical method with minimal matrix interference and high reproducibility for the tracing of active ayahuasca compound concentrations for the first time. This method is important as an auxiliary tool for the study of active compound effects in biological responses using different multi-omic platforms. © 2019 Elsevier B.V.