The chemical contamination in fruit and vegetables represents a challenging analytical issue, with tomatoes deserving to be investigated as they are fundamental components of the Mediterranean diet. Polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs) and nitro-PAHs contamination is of serious concern, due to particulate deposition and to uptake from contaminated soils and water. However, time-consuming, non-simultaneous and/or non-eco-friendly extraction procedures are typically used to investigate organic contamination in tomatoes, with nitro-PAHs that have not yet been studied. Based on these premises, this work reports the development of a QuEChERS-based approach, coupled with gas chromatography/mass spectrometry, for the simultaneous determination of 16 PAHs, 14 PCBs and 4 nitro-PAHs in three tomato cultivars. The effect of dichloromethane, cyclohexane and acetone, as well as of four clean-up phases were studied through the advanced combination of full factorial experimental design and multiple response optimization approaches. The final protocol, based on cyclohexane extraction followed by a double purification step with primary secondary amine and octadecyl silica and a sulfuric acid oxidation, led to 60–120% recoveries (RSD% < 15%). Good repeatability (inter-day precision <15%) and negligible matrix effect (<16%) were confirmed and the protocol was applied to the analysis of real tomato samples purchased in a local market.