A method for the simultaneous determination of pesticides, biopesticides and mycotoxins from organic products was developed. Extraction of more than 90 compounds was evaluated and performed by using a modified QuEChERS-based (acronym of Quick, Easy, Cheap, Effective, Rugged, and Safe) sample preparation procedure. The method was based on a single extraction with acidified acetonitrile, followed by partitioning with salts, avoiding any clean-up step prior the determination by ultra-high performance liquid chromatography/tandem quadrupole mass spectrometry (UHPLC-MS/MS). Validation studies were carried out in wheat, cucumber and red wine as representative matrixes. Recoveries of the spiked samples were in the range between 70 and 120% (with intra-day precision, expressed as relative standard deviation, lower than 20%) for most of the analysed compounds, except picloram and quinmerac. Inter-day precision, expressed as relative standard deviation, was lower than 24%. Limits of quantification were lower than 10μg kg⁻¹ and the developed method was successfully applied to the analysis of organic food products, detecting analytes belonging to the three types of compounds.