The development of agricultural policy is becoming a more and more difficult task. The number of factors which should be taken into account continues to grow, while at the same time there is an increased diversification of agricultural needs as well as higher consumer and taxpayer expectations. In this situation, the approach to agricultural policy-making used so far does not function properly. The final shape of the Common Agricultural Policy (CAP) in the new multiannual financing frameworks of the European Union has not been fully established yet. The work has been prolonged for many reasons. The current European Commission pays much attention to environmental and climate challenges, proposing the implementation of the European Green Deal strategy. One of the key elements of this development concept is the “Farm to Fork” strategy, which indicates the directions of transformation of food systems in the EU. A question arises whether the proposed shape of the EU strategy for agriculture is optimal in terms of challenges faced by this sector. Complexity economics may be an answer to this question, as it offers an approach to policy-making based on the recognition of the complexity of socio-economic systems and their specific dynamics requiring a specific shape of actions taken by the state.