This study outlines a comprehensive examination of risks and hazards in three egg sorting and packing stations, covering the entire process from supplier selection and evaluation to egg delivery in chain stores. The analysis is conducted within the framework of Codex Alimentarius and GFSI-integrated food safety programs. Salmonella is the greatest significant threat. To enhance the Hazard Analysis of Critical Control Points (HACCP), preparatory programs were incorporated into the quality management system (QMS) by monitoring and assessing the biological, chemical, and physical threats according to Code Alimentarius and further integrated into GFSI food safety programs, including food authenticity and food defense. The procedure offered sophisticated preventive tools, hand-on at any time, for eliminating, reducing, or mitigating the risks encountered in egg packing and sorting facilities.