Onion, Allium cepa L. is an economically and nutritionally important vegetable crop. Onion is one of the principal export crops in Egypt to various overseas markets. In this work, onion samples were collected from different locations in Assiut Governorate, Egypt. The occurrence of pesticide residues was analyzed by applying the Quick Easy Cheap Effective Rugged and Safe (QuEChERS) extraction method followed by LC-MS/MS analysis. Pesticide residues as many as 11 pesticide residues were common to all, such as spinosad (Spinosyns), acetamiprid (Neonicotinoids), deltamethrin and lambda-cyhalothrin (Pyrethroids), pendimethalin (Herbicide) and propamocarb, and fludioxonil (Fungicides). The most frequently found residue was pendimethalin, which was detected in samples from the Assiut, Abu Tig, and Manfalut regions, among others. Maximum residue levels (MRLs) were exceeded in several instances, most notably in multiple samples for pendimethalin (0.7 mg/kg), clethodim (0.7 mg/kg), and lambda-cyhalothrin (0.3 mg/kg) in El-Badari. In order to ensure food safety and compliance with international standards, the results emphasize the significance of strict monitoring, raise farmer awareness, and enhance pesticide management.