We conducted this study in order to assess the pesticide residues in vegetables and examine the related human health risk. Therefore, residues of 23 pesticides (organophosphates, organochlorines, acaricides, fungicides, and insecticides of biological origin) were analysed in the three main vegetable crops grown in Southern Nepal: 27 eggplant, 27 chilli and 32 tomato samples representing (i) conventional (N = 67) and ii) integrated pest management (IPM) fields (N = 19). Pesticide residues were found in 93% of the eggplant samples and in all of the chilli and tomato samples. Multiple residues were observed in 56% of the eggplant samples, 96% of chilli samples and all of the tomato samples. The range (µg/kg) of total detected pesticide residues in eggplants, chillies and tomatoes was 1.71–231, 4.97–507, 13.1–3465, respectively. The most frequently detected pesticides in these vegetables were carbendazim and chloropyrifos. Pesticide residues in 4% of the eggplant, 44% of the tomato and 19% of the chilli samples exceeded the EU maximum residue limits (MRLs). The residues of triazophos, omethoate, chloropyrifos and carbendazim exceeded the EU MRLs. Compared to chilli and eggplant crops, more carbendazim was sprayed onto tomato crops (p < 0.05). We assessed adolescent and adult dietary exposure using hazard quotient (HQ) and hazard index (HI) equations for the identified pesticides. HQ> 1 was observed for chloropyrifos, triazophos and carbendazim in eggplants; profenofos, triazophos, dimethoate, omethoate, chloropyrifos and carbendazim in tomatoes; and dichlorvos and chloropyrifos in chillies. Of all of the HQs, the highest acute HQ (aHQ) was for triazophos (tomato) in adolescents (aHQ=657) and adults (aHQ=677), showing the highest risks of dietary exposure. The cumulative dietary exposure showed a higher HI for organophosphates (HI>83) and a lower HI for organochlorines, acaricides and biological insecticides (HI<1). The concentration of pesticide residues in the vegetable crops from the IPM field was considerably lower, suggesting a greater ability of IPM systems to reduce the dietary risks from exposure to pesticides.