Sustainability is a systems problem with humans as integral elements of the system. However, sustainability problems usually have a broader scope than sociotechnical systems and therefore require additional considerations. This requires a fuller integration of complex systems understanding into the systems analysis toolset currently available to human factors and ergonomics. In this paper we outline these complex systems requirements necessary to tackle global problems such as sustainability and then assess how three common systems analysis tools (i.e. Accimap, System Theoretic Accident Mapping and Processes; and Cognitive Work Analysis) stand up against these revised criteria. This assessment is then further explored through applying two of these tools (i.e. Accimap and System Theoretic Accident Mapping and Processes) to a transnational food integrity system problem. This case study shows that no single systems analysis method can be used in isolation to help identify key insights for intervention and that new methods may need to be developed or existing methods need to be adapted to understand these dynamic, adaptive systems. The implications for the further development of systems analysis tools are discussed.