Food safety is a shared responsibility of all actors along the food supply chain. Changes in the primary production system can affect food safety hazards along the supply chain. This highlights the need for a framework that enables primary producers (i.e., farmers) to assess the potential food safety hazards and, if needed, to apply control measures. This paper presents a generic food safety assessment (GFSA) framework that has been developed based on Hazard Analysis and Critical Control Point (HACCP). The proposed framework was applied to a case study, i.e., the transition from sole cropping of oats to intercropping of oats with lupins. The application of the GFSA framework enabled the evaluation of potential changes in food safety hazards from this transition and the establishment of appropriate control measures. In addition, GFSA users can employ the results to support decision-making process. Our case study showed that implementing GFSA can be challenging for smallholder or individual farmers and may need coordinated action. Finally, effective and transparent communication is critical for managing food safety along the food supply chain, including when changes are implemented in primary production.