Soil can be contaminated by pesticide residues through agricultural practices, by direct application or through spray-drift in cultivations. The dissipation of those chemicals in the soil may pose risks to the environment and human health. A simple and sensitive multi-residue analytical method was optimized and validated for the simultaneous determination of 311 active substances of pesticides in agricultural soils. The method involves sample preparation with QuEChERS-based extraction, and determination of the analytes with a combination of GC-MS/MS and LC-MS/MS techniques. Calibration plots were linear for both detectors over the range of five concentration levels, using matrix-matched calibration standards. The obtained recoveries from fortified-soil samples ranged from 70 to 119% and from 72.6 to 119% for GC-MS/MS and LC-MS/MS, respectively, while precision values were <20% in all cases. As regards the matrix effect (ME), signal suppression was observed in the liquid chromatography (LC)-amenable compounds, which was further estimated to be negligible. The gas chromatography (GC)-amenable compounds showed enhancement in the chromatographic response estimated as medium or strong ME. The calibrated limit of quantification (LOQ) value was 0.01 μg g−1dry weight for most of the analytes, while the corresponding calculated limit of determination (LOD) value was 0.003 μg g−1d.w. The proposed method was subsequently applied to agricultural soils from Greece, and positive determinations were obtained, among which were non-authorized compounds. The results indicate that the developed multi-residue method is fit for the purpose of analyzing low levels of pesticides in soil, according to EU requirements.