In this comprehensive study, we evaluated the feasibility of using hydrogen instead of helium as a carrier gas in a GC-MS/MS system for pesticide residue analysis, spanning three matrices: pepper, tomato, and zucchini. Initial assessments focused on the ion source's chemical inertness, employing nitrobenzene as a benchmark to monitor the hydrogenation process. A method with a duration of less than 12 minutes was developed, achieving good chromatographic peak resolution attributable to the enhanced chromatographic performance of hydrogen as a carrier gas. The study emphasized the optimization of system parameters, testing various ion source temperatures, detector voltages, and injection volumes. Sensitivity assessments, based on the DG-SANTE criteria, indicated that the majority of compounds were identifiable at a concentration of 5 μg kg-1 (81% in tomato, 84% in pepper and 73% in zucchini). Detailed validation for reproducibility, matrix effects, and linearity across 150 pesticides unveiled generally favorable outcomes, with a notable majority of compounds displaying low matrix effects, satisfactory linearity ranges and good reproducibility with most compounds returning a relative standard deviation (RSD) below 10%. When applied to 15 real samples, the hydrogen-based system's performance was juxtaposed against a helium-based counterpart, revealing that results are very comparable between both systems. This comparative approach highlights hydrogen's potential as a reliable and efficient carrier gas in pesticide residue analysis for routine food control laboratories, overcoming difficulties resulting from the lack of helium supplies.