Barriers to food security and climate adaptation operate in complex and dynamic ways but are often perceived as static impediments to be overcome. In this study, we apply systems thinking for the assessment of barriers in agricultural decision-making for food security and climate adaptation. Using a mixed method approach of participatory simulation game design and causal loop diagrams, we explore the dynamic pathways through which barriers inhibit farmers from achieving food security and climate adaptation in Southern Mali. Results show that the key barriers in the region are financial, land, and climate-related barriers including unavailability of formal credit sources, high input prices, inadequate land access and ownership rights, time and labor constraints in collective vs individual plots, and climate risks such as early and late season droughts, high temperature, excessive rainfall, water scarcity, and pest incidences. These barriers operate in complex, interdependent, and dynamic ways where factors that act as enablers in one context can also function as barriers in another context. We see such interdependencies in three cases: i) access to interlocked credit and loans for cotton cultivation acts as enablers of income generation for male farmers but become barriers to female farmers who do not cultivate cotton ii) land ownership and land use rights for male farmers act as enablers for cultivation of income generating cash and food crops but acts as a barrier for female farmers by way of intra-household labor dynamics within collective plots iii) increase in land allocation to cotton and maize cultivation acts as enablers for increased household income but becomes a barrier to food security due to higher vulnerability to climate risks. Assessment of causal loop diagrams identified deep and shallow leverage points. Policies and interventions that focused on input subsidies and credit facilities are shallow leverage points where incremental changes will only lead to small improvements in farmers' livelihoods. Policies that support improved access and ownership of land to female farmers are deep leverage points that can potentially shift the dominant cropping pattern to more diversified and climate-resilient production.