Medicinal plants are important in the South African traditional healthcare system, the growth in the consumption has led to increase in trade through muthi shops and street vendors. Medicinal plants are prone to contamination with fungi and their mycotoxins. The study investigated multiple mycotoxin contamination using Ultra High Pressure Liquid Chromatography–Tandem Mass Spectrometry (UPLC-ESI-MS/MS) for the simultaneous detection of Aflatoxin B1 (AFB1), Deoxynivalenol (DON), Fumonisins (FB1, FB2, FB3), Nivalenol (NIV), Ochratoxin A (OTA) and Zearalenone (ZEN) in frequently sold medicinal plants. Medicinal plant samples (n = 34) were purchased and analyzed for the presence of eight mycotoxins. DON and NIV were not detected in all samples analyzed. Ten out of thirty-four samples tested positive for mycotoxins —AFB1 (10.0%); OTA (10.0%); FB1 (30.0%); FB2 (50.0%); FB3 (20.0%); and ZEN (30.0%). Mean concentration levels ranged from AFB1 (15 µg/kg), OTA (4 µg/kg), FB1 (7–12 µg/kg), FB2 (1–18 µg/kg), FB3 (1–15 µg/kg) and ZEN (7–183 µg/kg). Multiple mycotoxin contamination was observed in 30% of the positive samples with fumonisins. The concentration of AFB1 reported in this study is above the permissible limit for AFB1 (5 µg/kg). Fumonisin concentration did not exceed the limits set for raw maize grain (4000 µg/kg of FB1 and FB2). ZEN and OTA are not regulated in South Africa. The findings indicate the prevalence of mycotoxin contamination in frequently traded medicinal plants that poses a health risk to consumers. There is therefore a need for routine monitoring of multiple mycotoxin contamination, human exposure assessments using biomarker analysis and establishment of regulations and standards.