In recent years, the official authorities in Chile have reported transgressions in the maximum residue levels of pesticides in fresh vegetables. There is no official information about traceability, pesticide levels, and potential health risks. The aim of this study was to analyse pesticide residues and their corresponding dietary risk assessments in tomatoes from supermarkets in the Metropolitan Region. Pesticides were extracted using the Quick, Easy, Cheap, Effective, Rugged and Safe, QuEChERS method, and their concentrations were determined by using chromatography with HPLC-FL/UV and GC-MS/ECD/NPD, following the Analytical Quality Control and Method Validation Procedures for Pesticides Residues Analysis in Food and Feed, SANTE guide and ISO 17025:2017 standard. In addition, a dietary risk assessment was carried out by comparing Chilean data to international references. The results reported that 9% of the samples had pesticide residue levels above the maximum residue levels permitted in Chile. All the scenarios evaluated revealed the highest estimated daily intake and hazard quotients for methamidophos and chlorpyrifos. Both the active substances used were acetylcholinesterase inhibitors and were neurotoxic under chronic risk assessment. The results showed the highest chronic hazard index in the Chilean scenario for all age groups and genders. The evidence obtained revealed that methamidophos, methomyl, and chlorpyrifos should be restricted for their use in Chilean agriculture.