In this work, a new method based on nanoflow LC with high-resolution MS was developed for the determination of eight pesticides in pollen and nectar samples, including neonicotinoid insecticides and other selected pesticides commonly found in bees and beeswax. Detection was undertaken with a hybrid quadrupole-Orbitrap mass spectrometer (Q Exactive™) equipped with a commercial nanospray ion source. The extraction of pesticides from pollen samples was performed by a modified micro-QuEChERS method scaled down to Eppendorf tubes, whereas nectar samples were simply diluted with a water-methanol (95 + 5, v/v) solution. Good linearity (>0.999 in all cases) was obtained between 0.05 and 500 µg/kg and between 0.04 and 400 µg/kg for pollen and nectar, respectively. Recovery rates in pollen ranged from 85 to 97%, with RSDs <12%. Matrix effect was evaluated and showed negligible effects for all studied pesticides. The lowest concentration levels tested and validated were 0.5 and 0.4 µg/kg for pollen and nectar matrixes, respectively. In addition, selected incurred samples were studied, obtaining several positive findings in pollen and nectar samples, demonstrating the sensitivity and applicability of the proposed method.