Background: Mycotoxins are big concerns in food safety. Analytical methods are important for the evaluation of mycotoxins in different food commodities. Objective: In this study, stable isotope dilution assay (SIDA) was compared with a matrix-matched calibration method for the quantification of mycotoxins in four different commercially available commodities and two reference materials. Methods: All samples were extracted with water-acetonitrile (50+50, v/v), followed by filtration and LC-tandem MS analysis. Results: SIDA calibration accuracies ranged from 78.6 to 112% with relative SDs (RSDs) ≤16% across all four matrices. The majority of the recoveries across all matrices ranged from 70 to 120% with RSDs <11%. Of the four mycotoxins in the reference materials analyzed, only three had 13C-internal standard (IS), whereas the fourth was quantified using a closely eluting 13C-IS for a different mycotoxin. Mycotoxins paired with their corresponding 13C-IS had accuracies >90%, whereas accuracies for the mismatched mycotoxin/13C-IS were <14%. Conclusions: When 13C-IS are not available, matrix-matched calibration was also evaluated as an alternative to quantitating target mycotoxins. The use of 13C-IS is the best way to dynamically account for prevalent matrix effects, but matrix matching provides a viable alternative. Highlights: The study compared SIDA and matrix-matched calibration methods in terms of recovery, efficiency, advantages, and limitations for LC-MS based mycotoxin analysis.