As the pesticide and its metabolite residues in processed fruits could become a significant route of human exposure. The work presented herein focuses on developing a feasible quick, easy, cheap, effective, rugged, and safe method with improved extraction and cleanup system for the determination of imidacloprid, acetamiprid, thiamethoxam, and clothianidin (a metabolite of thiamethoxam) in canned fruits. The low toxic solvent ethanol was used to extract the analytes, and ammonium sulfate was used to promote phase separation. Moreover, the carboxylated multi‐walled carbon nanotube acted as the clean‐up sorbent for the removal of high solubility impurities. The proposed method was validated with fortified real samples at different concentration levels (20–200 μg/kg). Recoveries obtained from three spiked levels (20, 50, and 200 μg/kg) ranged from 74.9 to 86.4% with relative standard deviations of the intra‐day and inter‐day in the range of 0.8–5.5 and 2.0–7.1%, respectively. The limits of detection ranged from 0.2 to 0.5 and 0.2 to 0.6 μg/kg for orange and peach, respectively. The results demonstrated that the proposed method could be considered appropriate, and comparatively lower toxic for the analysis of neonicotinoid pesticide residues in canned fruit.