Eco-functional intensification is understood as building synergies in multi-functional and resilient agricultural systems in harmony with their surrounding environment and human systems, to the benefit of diversified production of food and beyond, as in, for example, ecosystem services. Integration of animals into eco-functionally intensified agricultural systems to enhance agricultural, ecological and social systems, can contribute to driving a future sustainable development of organic agricultural and food systems. This approach may respond to challenges of an increasing industrialization of livestock in the global north, a process which has led to heavy reliance on external inputs, and, to a large extent, a detachment of animals from farming systems, especially in the global south. Animals are living sentient beings, but often not acknowledged as such. Complex, well-integrated systems can be organized so that they support the health and welfare of animals, and let these animals be valuable resources within the farming system. There must be an emphasis on diverse genetic inheritance and locally adapted species. Complex systems require complex knowledge which must be continuously developed to respond to current challenges in constantly changing environments, e.g., climate change. A necessary driver in transition towards more eco-functionally intensified agricultural and food systems is a governance system which protect the actors without a voice, e.g., ecosystems, pollinators, animals, and future generations through regulation of consumption patterns, flow of external inputs, and resource use. This requires a change in attitudes both acknowledgment of the importance of protecting the environment, consumption, resource use; and seeing agricultural systems as necessary and valuable contributors to nourishing both people and the earth.