Irrespective of the existence of potentially pathogenic organisms carried by animals, foods of animal origin remain the prime nutrition of humans world-wide. As such, food safety continues to be a global concern primarily to safeguard public health and to promote international trade. Application of integrated risk-based quality assurance procedures on-farm and at slaughterhouses plays a crucial role in controlling hazards associated with foods of animal origin. In the present paper we examine safety assurance systems and associated value chains for foods of animal origin based on historical audit results of some Southern African countries with thriving export trade in animal products, mainly to identify areas for improvement. Among the key deficiencies identified were: i) failure to keep pace with scientific advances related to the ever-changing food supply chain; ii) lack of effective national and regional intervention strategies to curtail pathogen transmission and evolution, notably the zoonotic Shiga toxin-producing Escherichia coli; and iii) a lack of effective methods to reduce contamination of foods of wildlife origin. The introduction of foods of wildlife origin for domestic consumption and export markets seriously compounds already existing conflicts in legislation governing food supply and safety. This analysis identifies gaps required to improve the safety of foods of wildlife origin.