The use of medicinal herbs has increased significantly. However, the presence of pesticide residues and mycotoxins in medicinal herbs has generated constant discussion and concern among regulatory agencies. Developing and validating an analytical method for determining pesticides and mycotoxins in medicinal plants is challenging due to the naturally occurring substances in these plants. The purpose of this work was to develop and to optimize a sensitive, accurate, precise, effective QuEChERS method for simultaneous determination of over 160 pesticide and mycotoxin residues in complex medicinal plant matrices using LC-TQ-MS/MS. A comprehensive comparison of clean-up procedures and other parameters was conducted to achieve this goal. The validation procedure was performed according to SANTE 11312/2021. More polar analytes, such as acephate, methamidophos and omethoate, presented a higher negative matrix effect in both Melissa officinalis L. and Malva sylvestris L. However, other molecules, such as spirodiclofen, showed a 24% signal enhancement in M. officinalis and a 46% signal suppression in M. sylvestris, indicating that a representative matrix-matched calibration would lead to inaccurate quantification of the analyte. Accuracy and precision were satisfactory according to SANTE 11312/2021 for 157 pesticide residues and mycotoxins in M. officinalis and for 152 molecules in M. sylvestris. LOQs at 10 µg kg-1 were achieved for 117 pesticides in M. officinalis and 99 pesticides in M. sylvestris. Among the mycotoxins, all four aflatoxins (B1, B2, G1 and G2) presented LOQs of 5 µg kg-1, and ochratoxin A had an LOQ of 10 µg kg-1 in M. officinalis. The same LOQ values were shown for these mycotoxins in M. sylvestris, except for aflatoxin B2 and ochratoxin A, which had LOQs of 20 µg kg-1. Moreover, in Southern Brazil, there has been no previous study on mycotoxin and pesticide contamination in medicinal herbs. Therefore, the application of this method was assessed through the analysis of forty-two real samples. Imidacloprid was found in M. officinalis, and methyl pirimiphos was found in M. sylvestris. The proposed method not only serves as a helpful tool for routine monitoring but also offers a basis for further research on risk assessment and control in food safety.