This study aimed to optimize and validate a multi-residue method for identifying and quantifying pesticides in honey by using both gas and liquid chromatographic separation followed by mass spectrometric detection. The proposed method was validated to detect 168 compounds, 127 of them by LC-MS/MS (liquid chromatography tandem mass spectrometric detection) and 41 by GC-MS/MS (gas chromatography tandem mass spectrometric detection). The limit of detection (LOD) and limit of quantification (LOQ) values for the analytes determined by LC-MS/MS were 0.0001–0.0004 mg/kg and 0.0002–0.0008 mg/kg, respectively. For GC-MS/MS analyses, the LOD and LOQ values were 0.001–0.004 mg/kg and 0.002–0.008 mg/kg. In total, 33 samples of commercial honey produced by apiaries in six Brazilian states were analyzed with the validated method. Residual amounts of 15 analytes were detected in 31 samples (93.9%). The method described in the present study was able to detect an extensive and broad range of pesticides with very high sensitivity.