School meal service workers may face an increased risk of lung cancer due to the nature of their work. This study aims to assess environmental exposure levels during occupational cooking among these workers in Seoul, Republic of Korea, and to examine the associations with carcinogen-associated biomarkers. Additionally, the study seeks to verify lung carcinogenesis through experiments using lung organoids treated with carcinogens, such as polycyclic aromatic hydrocarbons (PAHs) and particulate matter. Here, we introduce the study protocol and outline our research strategies. This etiome study employs molecular epidemiological approaches involving at least 200 school meal service workers from 25–30 school cafeterias in Seoul, as well as in vitro lung organoid experiments. The study includes a questionnaire survey to analyze workers’ occupational environments, focusing on exposure to hazardous substances such as cooking oil fumes and assessing the use of personal protective equipment (e.g., masks) and the presence of ventilation systems. We measure molecular epigenomic biomarkers, including PAH adducts and metabolites along with methylation markers, in the exposure and control groups. Additionally, lung organoid experiments are performed to investigate the potential for lung cancer development due to respiratory carcinogen exposure in cooks. This study is expected to contribute to health risk assessments and the establishment of preventive strategies for meal service workers.