Logistics as the link between the different stages of the food supply chain can, due to its complexity, provide multiple opportunities for food / feed contamination along global commodity flows. Considering comprehensive international food safety regulations, such as the Regulation (EU) 2019/1381, risk assessment in the field of consumer health protection requires specific approaches determining the impact of logistics on food safety. To identify critical dimensions and corresponding critical factors for food safety in global commodity flows and map complex interactions, we conducted a case study on mycotoxin contamination of agricultural commodities. Accordingly, we interviewed 24 stakeholders directly or indirectly involved in the European and global purchasing and logistics sector of agricultural commodities. Based on the outcome of the interviews, the most relevant dimensions are Logistical processes, Food safety measures, Human factor, Disruptions and shifts, Logistics related conditions, Cooperation, Main Characteristics of the procurement sector and Port characteristics. Food safety risks along global commodity flows are not solely attributable to the logistics sector per se. In particular, Food safety measures (e.g. Quality management and Sampling) that are not adapted to the logistics sector, as well as varying Logistics related conditions (e.g. Infrastructure and Standards) have proven to be major food safety challenges. By providing an overall picture of global commodity flows, the study contributes to reduce current uncertainties in risk assessment. The identified food safety challenges in the logistics sector need to be addressed holistically throughout the entire supply chain and in cooperation with food safety authorities.