Agroecology pays careful attention to the design of diversified systems that selectively combine annual and perennial crops, livestock and aquatic animals, trees, soils, water and other components on farms and agricultural landscapes to enhance synergies in the context of an increasingly changing climate.

Building synergies in food systems delivers multiple benefits. By optimizing biological synergies, agroecological practices enhance ecological functions, leading to greater resource-use efficiency and resilience. For example, globally, biological nitrogen fixation by pulses in intercropping systems or rotations generates close to USD 10 million savings in nitrogen fertilizers every year, while contributing to soil health, climate change mitigation and adaptation. Furthermore, about 15 percent of the nitrogen applied to crops comes from livestock manure, highlighting synergies resulting from crop–livestock integration. In Asia, integrated rice systems combine rice cultivation with the generation of other products such as fish, ducks and trees. By maximising synergies, integrated rice systems significantly improve yield, dietary diversity, weed control, soil structure and fertility, as well as providing biodiversity habitat and pest control.

At the landscape level, synchronization of productive activities in time and space is necessary to enhance synergies. Soil erosion control using Calliandra hedgerows is common in integrated agroecological systems in the East African Highlands. In this example, the management practice of periodic pruning reduces tree competition with crops grown between hedgerows and at the same time provides feed for animals, creating synergies between the different components. Pastoralism and extensive livestock grazing systems manage complex interactions between people, multi-species herds and variable environmental conditions, building resilience and contributing to ecosystem services such as seed dispersal, habitat preservation and soil fertility.

While agroecological approaches strive to maximise synergies, trade-offs also occur in natural and human systems. For example, the allocation of resource use or access rights often involve trade-offs. To promote synergies within the wider food system, and best manage trade-offs, agroecology emphasizes the importance of partnerships, cooperation and responsible governance, involving different actors at multiple scales.