In this study, a method was implemented for the determination of chlorpyrifos, a very toxic pesticide according to the EPA and EFSA used in agriculture, in samples of beekeeping products. Samples were extracted using the QuEChERS method according to the official method of AOAC 2007.01 and determined by liquid chromatography-tandem mass spectrometry (LC–MS/MS). The results show that the data fit a linear model with a coefficient of determination (r2) of 0.9896 in a concentration range between 0.0015 to 1.28 ppm using a commercial standard. The samples presented higher concentrations of the pesticide in bee pollen than in honey, just as there was a higher amount of the pesticide in the rural samples compared to the urban samples. This work demonstrated that the implemented method is useful and reliable for the monitoring of this type of pesticides in samples of bee products to control their quality.