Exposure of honeybee (Apis mellifera L.) to pesticides disturbed normal physiological and behavioral functions required for normal foraging and colony maintenance. The present study was aimed towards establishing the mean lethal concentration (LC50) of three pesticides viz. carbamate (carbaryl), organophosphate (chlorpyrifos) and neonicotinoid (imidacloprid) in honeybees through feeding bioassay laboratory trial. Deleteriousness was confirmed through mortality rate, number of survival bees, acetylcholinesterase (AChE), total protein (TP) levels, AChE gene transcription level, and gut tissues histological analysis of exposed honeybees. Mean mortality rate was calculated for 96 h interval at three different concentrations of tested pesticides (5, 2.5, and 1.25 mg L−1), and LC50 values calculated for 48 and 96 h interval. AChE enzyme and TP level are determined by ELIZA and spectrophotometer, respectively. Results revealed that imidacloprid had the lowest LC50 (0.477 ng/bee) values as compared with carbaryl and chlorpyrifos. High mortality rate was observed at highest dose, being impidacloprid have more lethal effects as compared with other pesticides. Similarly, biochemical analysis revealed that imidiacloprid and chlorpyrifos significantly (P ≤ 0.05) increased AChE and TP levels, whereas carbaryl significantly (P ≤ 0.05) decreased them. Similarly, probe based RT qPCR revealed that imidacloprid and chlorpyrifos treatments significantly (P ≤ 0.05) enhanced the AChE level whereas carbaryl decreased it. Histological analysis showed that the gut tissues of honeybees exposed to pesticide treatment had substantial morphological abnormalities. In a nutshell, imidacloprid, carbaryl and chlorpyrifos have substantial toxic effects on all the study attributes of honeybees with imidacloprid being most toxic.