The combined use of gas chromatography (GC) and ultrahigh-pressure liquid chromatography (UHPLC), both coupled to time-of-flight mass spectrometry (TOF MS), has been explored in this work for the investigation of several cases of honeybee poisoning. The procedure applied involves a previous extraction with acetone followed by liquid-liquid extraction with dichloromethane. Both techniques, GC-TOF MS and UHPLC-(Q)TOF MS, have been applied to discover the presence of compounds that might be responsible of honeybee deaths. The application of a nontarget methodological approach to a first case of poisoning allowed the detection of the insecticide coumaphos at high concentration levels in the samples. The presence of possible metabolites of this organophosphorus insecticide was investigated by using both techniques. UHPLC-(Q)TOF MS showed its higher applicability in this case, as most of the metabolites were more polar than the parent compound. Four metabolites were identified by UHPLC-(Q)TOF MS, whereas only two of them were found by GC-TOF MS. The developed methodology was applied to other subsequent poisoning cases in which insecticides such as coumaphos, thiamethoxam, pyriproxyfen, and chlorfenvinphos were identified by both techniques, whereas GC-TOF MS also allowed the detection of fenitrothion and methiocarb. In all positive cases, the confirmation of the presence of the compound detected was feasible by means of accurate mass measurements of up to five ions together with their ion ratio evaluation.