The use of medicinal plants concomitantly with conventional drugs can result in herb-drug interactions that cause fluctuations in drug bioavailability and consequent therapeutic failure and/or toxic effects. The CYP superfamily of enzymes plays an important role in herb-drug interactions. Among CYP enzymes, CYP3A4 and CYP2D6 are the most relevant since they metabolize about 50% and 30% of the drugs on the market, respectively. Thus, the main goal of this study was to evaluate the occurrence of in vitro interactions between medicinal plant extracts and drug substrates of CYP3A4 and CYP2D6 enzymes. Standardized extracts from nine medicinal plants (Bauhinia forficata, Cecropia glaziovii, Cimicifuga racemosa, Cynara scolymus, Echinacea sp., Ginkgo biloba, Glycine max, Ilex paraguariensis, and Matricaria recutita) were evaluated for their potential interactions mediated by CYP3A4 and CYP2D6 enzymes. Among the extracts tested, C. glaziovii (red embaúba) showed the most relevant inhibitory effects of CYP3A4 and CYP2D6 activity, while I. paraguariensis (yerba mate) inhibited CYP3A4 activity. Both extracts were chemically analyzed by UPLC-MS/MS, and these inhibitory effects could lead to clinically potential and relevant interactions with the drug substrates of these isoenzymes.