Management of weeds is the major challenge to the success of onion. Chemical weed control has been intensively used to reinforce crop yield; however, even selective herbicides can potentially interfere with biochemical and physiological changes in onion. A field experiment was conducted to evaluate the efficacy of different herbicides pendimethalin, oxyfluorfen and quizalofop-ethyl individually and in combinations on weed control efficiency, yield attributes, changes in photosynthetic pigments, membrane injury and persistence of herbicides in onion. The combined application of oxyfluorfen and quizalofop-ethyl efficiently influenced the weed density and biomass causing higher yield and net returns. The application of oxyfluorfen recorded highest weed control efficiency, while a decline in photosynthetic pigments caused lesser yield. The results of QuEChER method of liquid chromatography tandem mass spectrometry (LC-MS/MS) revealed that herbicide residue did not find in both leaves and bulb in any treatment.