Controlling pesticide residues in food has been always a concern globally. It is recommended to use certified reference materials (CRM) or reference materials (RM) in pesticide analysis to validate analytical methods and assess the quality of the measurement results. A comprehensive study on production, storage, transportation, and utilization of an RM of pesticide residues (Difenoconazole, Imidacloprid, Acetamiprid, Indoxacarb, Profenofos, Buprofezin) in tomato was conducted. After comparing two production processes of freezing and freeze-drying, the freeze-drying production process was concluded to be superior. The RM production and characterization process is in accordance with ISO 17034:2016 and ISO guide 35:2017-08. The concentrations of 6 pesticides in the RM are around their Codex maximum residue limits. At a storage temperature of 4°C, freeze-dried RM are predicted to be stable for all six pesticides for at least 548 days, while at a temperature of − 20°C, the shelf life was at least 696 days.