The study was designed to get a real time picture of pesticide residues in tomato samples from the fields of two districts of Khyber Pakhtunkhwa and the markets of Islamabad, Pakistan. A citrate buffered QuEChERS method was validated for forty-nine multiclass pesticides belonging to carbamates, neonicotinoids, organophosphates, pyrethroids, triazines and triazoles on LC-MS/MS. The method’s limits of detection and the quantification with the validated method ranged from 0.001 to 0.01 mg/kg and 0.01–0.1 mg/kg, respectively. Fifty one samples were analyzed with the validated method, and 58.8 % (n = 30) of the analyzed samples were found contaminated. Out of these contaminated samples, 83.3 % (n-25) were field samples, and 16.7 % (n = 5) were market samples. Four (7.8 %) field samples were found non-compliant with the European Union’s Maximum Residue Limits (EU-MRLs). The frequently detected pesticides were imidacloprid and tebuconazole. Thiamethoxam, tebuconazole, pyraclostrobin, metalaxyl, and chlorpyrifos, were the pesticides that exceeded the EU-MRLs. The residues of detected pesticides were found to pose a very low health risk to consumers.