In this study we show that a nonaqueous capillary electrophoresis mass spectrometry (NACE-MS) method carefully optimized by a design of experiment can be applied to a very large number of alkaloids in different plant extracts. It is possible to characterize the pattern of the psychoactive alkaloids in several plant samples and preparations thereof, each presenting different challenges in their analysis. The method is shown to be able to separate structurally closely related substances, diastereomers and further isobaric compounds, to separate members of different alkaloid classes within one run and to tolerate significant matrix load. A comparison with methods presented in the literature reveals that a near-generic NACE-MS method for the fast profiling of alkaloids in forensically relevant plant samples has been developed.