In this study, a new method for the determination of 12 nitroimidazoles and their hydroxymetabolites (metronidazole, hydroxymetronidazole, dimetridazole, ronidazole, hydroxydimetridazole, ipronidazole, hydroxyipronidazole, carnidazole, ornidazole, secnidazole, ternidazole, tinidazole) in beeswax has been developed and validated. The optimized sample preparation procedure included melting and dilution of beeswax in a mixture of n-hexane and isopropanol followed by extraction with 2% acetic acid. The extracts were purified on strong cation exchange based solid-phase extraction cartridges and evaporated in a vacuum system with vortex motion. The separation and detection of the nitroimidazoles in the beeswax extracts were achieved within 12 min by liquid chromatography tandem mass spectrometry using a pentafluorophenyl analytical column and applying a gradient elution with acetonitrile and 0.01% acetic acid as mobile phases. The method performance characteristics were evaluated at three concentration levels (1, 2, and 5 μg/kg) and the method was found to be suitable for determination of all tested nitroimidazoles. The limits of detection and quantification were 0.2–0.5 and 0.5–1 μg/kg, respectively. The recoveries varied from 71.2 to 104.9% while the relative standard deviations were less than 13.8% under the intermediate precision conditions.