World food supply is crucial to the well-being of every human on the planet in the basic sense that we need food to live. It also has a profound impact on the world economy, international trade and global political stability. Furthermore, consumption of certain types and amounts foods can affect health, and the choice of livestock and plants for food production can impact sustainable use of global resources. There are communities where insufficient food causes nutritional deficiencies, and at the same time other communities eating too much food leading to obesity and accompanying diseases. These aspects reflect the utmost importance of agricultural production and conversion of commodities to food products. Moreover, all factors contributing to the food supply are interdependent, and they are an integrative part of the continuously changing, adaptive and interdependent systems in the world around us. The properties of such interdependent systems usually cannot be inferred from the properties of its parts. In addressing current challenges, like the apparent incongruences of obesity and hunger, we have to account for the complex interdependencies among areas such as physics and sociology. This is possible using the complex system approach. It encompasses an integrative multi-scale and inter-disciplinary approach. Using a complex system approach that accounts for the needs of stakeholders in the agriculture and food domain, and determines which research programs will enable these stakeholders to better anticipate emerging developments in the world around them, will enable them to determine effective intervention strategies to simultaneously optimise and safeguard their interests and the interests of the environment.