Pesticides are broadly used to improve food safety, although they can lead to adverse health effects on consumers. Various food processing approaches, at the industrial or domestic level, have been found to highly reduce the amount of pesticide residues in most food materials. In this work, samples of raw tomatoes were collected directly from the field and processed at the industrial level to produce purée, triple concentrated paste, fine pulp, and diced tomatoes. A multiresidue method based on a modified QuEChERS (Quick, Easy, Cheap, Effective, Rugged e Safe) sample preparation, followed by liquid chromatography-tandem mass spectrometry analysis (LC-MS/MS) for the assessment of 116 pesticides residues, was used. The analytical method has been validated according to SANTE indications. The recovery yields ranged from 75.5% to 115.3%, repeatability (RSDr) ranged from 3.4% to 18.3%, while reproducibility (RSDwR) ranged from 5.4% to 19.8%. The limit of quantifications (LOQs) ranged from 2.35 µg kg−1 for benthiavalicarb to 6.49 µg kg−1 for allethrin. A total of 159 raw tomato samples were collected from the field. The analysis showed the presence of 46 pesticides with azoxystrobin and chlorantraniliprole the most represented. On the other hand, all industrially processed samples showed values ≤ LOD, confirming that post-harvest processes can lead to a decrease in pesticide residues from agricultural commodities.