Introduction: During intercontinental shipping, freight containers and closed transport devices are applied. These ambiences can be polluted with harmful chemicals that may accumulate in poorly ventilated environments. The major pollutants are fumigants as well as volatile organic compounds. While handling cargos, workers can be exposed to these chemicals, frequently without adequate occupational health and safety precautions. Aim of the study: To investigate presumed occupational chemical exposures and their experienced health impacts, as well as the related KAP among workers at Hungarian logistics companies. Methods: A cross-sectional questionnaire survey was conducted among potentially exposed warehouse workers and office workers as controls at Hungarian logistics companies (1) to investigate the health effects of chemical pollutants occurring in closed environments of warehousing and (2) to collect information about the knowledge of workplace chemical exposures as well as the occupational health and safety precautions applied. Results: Pre-existing medical conditions did not show significant differences between the working groups. Numbness or heaviness in the arms and legs (AOR = 3.99; 95% CI = 1.72–9.26) and dry cough (AOR = 2.32; 95% CI = 1.09–4.93) were significantly associated with working in closed environments of transportation and storage, while forgetfulness (AOR = 0.40; 95% CI = 0.18–0.87) and sleep disturbances (AOR = 0.36; 95% CI = 0.17–0.78) were significantly associated with employment in office. Warehouse workers who completed specific workplace health and safety training had more detailed knowledge related to this workplace chemical issue, and they were significantly more likely to use certain preventive measures against the pollutants. Conclusions: Warehouse workers at logistics companies may be exposed to different chemical pollutants and the related health risks may remain unknown. Applied occupational health and safety measures at logistics companies are not adequate enough to manage this workplace chemical issue, which warrants effective preventive strategies to protect workers’ health.