In this study, we aimed to establish a method for determination of multiple mycotoxins such as aflatoxins, ochratoxin A, and zearalenone in red pepper powder samples based on the quick, easy, cheap, effective, rugged, and safe (QuEChERS) approach for extraction and cleanup, with detection and quantification by high-performance liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) in both positive- and negative-ion modes. The developed LC-MS/MS analytical method was compared with an enzyme-linked immunosorbent assay (ELISA) to improve the reliability of our developed method. The linearity, precision, and accuracy were validated for the LC-MS/MS methods. The results obtained with the LC-MS/MS were linear, with a correlation coefficient (R) of >0.998. The limits of detection and quantification for mycotoxins were 0.07 to 0.71 μg/kg and 0.20 to 1.81 μg/kg, respectively. Intra- and interday precision tests (expressed as the relative standard deviation) for each analyte were 1.58 to 5.97% and 0.97 to 9.01%, respectively. Average recoveries were 85.70 to 94.99%. The validation results for the ELISA were linear (R > 0.995), and recoveries were 77.13 to 93.93%. Both analytical methods were applied to determine the presence of mycotoxins in commercial red pepper powder samples from South Korea. Four of the total 56 samples were contaminated with aflatoxins, and 6 samples were contaminated with ochratoxin A; these results were consistent for the two methods (P > 0.05). Therefore, our developed LC-MS/MS with QuEChERS approach for determination of multiple mycotoxins may be useful for controlling the quality and safety of red pepper powder.