Globalization of agricultural trade has led to food supply chains becoming increasingly complex. A high number and diversity of entities, processes, and localisations can create food safety risks and vulnerabilities at all stages of the food supply chain. To date, food safety measures have focused mainly on production, processing, and retail. However, the dimension of commodity flows embedded in the logistics sector, which links the main stages, has largely been neglected. The resulting knowledge gaps pose a challenge to risk assessors concerned with consumer health protection. To map the research area of global commodity flows and investigate their impact on food safety, a conceptual framework (CF) was developed using agricultural bulk commodities (ABC) as an example. The construction of the CF is based on a qualitative text analysis of multidisciplinary literature, adapted from the Grounded Theory approach. Here we determined and illustrated different levels of the main concepts inside and outside of ABC flows relevant for the investigation of logistics in terms of food safety. The main internal concepts are Key processes and Management, Key actors and Cooperation, Routes and Nodes, and their Quality and Capacity. The external concepts can be divided into Logistics-related conditions and the associated Diversity, as well as Drivers of change associated with the Dynamics of globalization. The developed CF represents a first model for holistically investigating logistics in terms of food safety by defining, structuring, and delimitating logistics as a new field of investigation in risk assessment. It offers suitable concepts and application-oriented theories related to food safety that serve as a basis for empirical studies, such as the identification of critical factors in the logistics sector. Further, it serves as an aid to practitioners in dealing with complex food safety problems in the context of risk management.