This article analyzes the impact of chemical agents used during the storage of vegetables on the food safety management system. It systematically evaluates possible chemical, microbiological, and organoleptic changes resulting from the use of antimicrobial and antifungal substances, preservatives, ethylene inhibitors, and oxidation-based technologies commonly applied in storage. The research approach follows ISO 22000 requirements, encompassing the stages of hazard identification, assessment, and control, as well as the recommendations of the Codex Alimentarius and national regulatory documents (O‘zDSt). The paper highlights permissible maximum residue levels, critical control points, traceability, and verification mechanisms. Methodological approaches such as chromatographic and spectral analyses and microbiological indicators are presented to assess the residual quantities of chemical agents, the potential accumulation of nitrates and heavy metals, and the preservation of beneficial bio-oils, vitamins, and antioxidants.