Aflatoxins and ochratoxin A can occur naturally in a variety of food products via pre- and post-harvest contamination mechanisms and are regulated worldwide. Consumption of mycotoxin contaminated foods can pose a significant risk to human health. Herein we describe three different methods for specific food commodities: - Aflatoxins in groundnuts, pistachio, and hazelnuts using Aflatest WB cleanup - Ochratoxin A in roasted coffee and cocoa using OchraTest WB cleanup - Aflatoxins and ochratoxin A in black pepper using AflaOchra cleanup All the mentioned methods have been internally validated using spiked samples as well as naturally contaminated reference materials, where available, and are based upon a solid-liquid extraction, followed by a trap-and-release step using immunoaffinity chromatography (IAC) and LC-MS/MS analysis. The methods provide optimal performance in terms of trueness and repeatability, with method LOQs as low as 0.050 μg/kg for aflatoxins and 0.4 μg/kg for ochratoxin A. The use of IAC clean-up is particularly advantageous as it allows the use of calibration curves based on solvent standards, removing the need to prepare closely matrix-matched calibration standards and without the need for (isotopically labeled) internal standards. Moreover, it provides excellent recoveries (in the range 71–108%, mean 90%) due to the highly specific antibody-based binding, and minimizes the potential matrix effects, thus making it suitable to be coupled with tandem mass spectrometry.