The possible presence of contaminants, pesticide residues and mycotoxins, in agricultural commodities is a critical issue for food safety, causing great concern. In this work, a simple and rapid analytical method employing liquid chromatography–tandem mass spectrometry (LC-MS/MS) was developed for the simultaneous determination of pesticide residues and mycotoxins in apples. Microwave-assisted extraction (MAE) was used for sample preparation. The MAE protocol was optimized after evaluating the effects of the following extraction parameters: (a) extraction solvent, (b) acidic environment, (c) temperature, and (d) extraction time. The multiresidue MAE-LC-MS/MS method was validated for linearity, accuracy (bias and precision), limits of detection (LODs), limits of quantification (LOQs), and matrix effect. The validation of the method was carried out according to the SANTE/12682/2019 document. The method demonstrated good linearity with R2 ≥ 0.99, acceptable accuracy in the recovery rate range 70–116%, acceptable interassay precision with RSD% ≤ 20, and low LODs and LOQs in the ranges 0.005–0.015 μg/g and 0.01–0.03 μg/g, respectively. Matrix effects were observed only for the 25% of the analytes. The performance of the MAE-LC-MS/MS method was compared to that of the QuEChERS sample preparation method, and the MAE-LC-MS/MS method proved to be rapid and effective.