Agroecological systems are highly diverse. From a biological perspective, agroecological systems optimize the diversity of species and genetic resources in different ways. For example, agroforestry systems organize crops, shrubs, livestock and trees of different heights and shapes at different levels or strata, increasing vertical diversity. Intercropping combines complementary species to increase spatial diversity. Crop rotations, often including legumes, increase temporal diversity. Crop–livestock systems rely on the diversity of local breeds adapted to specific environments. In the aquatic world, traditional fish polyculture farming, Integrated Multi-Trophic Aquaculture (IMTA) or rotational crop-fish systems follow the same principles to maximising diversity.

Increasing biodiversity contributes to a range of production, socio-economic, nutrition and environmental benefits. By planning and managing diversity, agroecological approaches enhance the provisioning of ecosystem services, including pollination and soil health, upon which agricultural production depends. Diversification can increase productivity and resource-use efficiency by optimizing biomass and water harvesting.

Agroecological diversification also strengthens ecological and socio-economic resilience, including by creating new market opportunities. For example, crop and animal diversity reduces the risk of failure in the face of climate change. Mixed grazing by different species of ruminants reduces health risks from parasitism, while diverse local species or breeds have greater abilities to survive, produce and maintain reproduction levels in harsh environments. In turn, having a variety of income sources from differentiated and new markets, including diverse products, local food processing and agritourism, helps to stabilize household incomes.

Consuming a diverse range of cereals, pulses, fruits, vegetables and animal-source products contributes to improved nutritional outcomes. Moreover, the genetic diversity of different varieties, breeds and species is important in contributing macronutrients, micronutrients and other bioactive compounds to human diets. For example, in Micronesia, reintroducing an underutilized traditional variety of orange-fleshed banana with 50 times more beta-carotene than the widely available commercial white-fleshed banana proved instrumental in improving health and nutrition.

At the global level, three cereal crops provide close to 50 percent of all calories consumed, while the genetic diversity of crops, livestock, aquatic animals and trees continues to be rapidly lost. Agroecology can help reverse these trends by managing and conserving agro-biodiversity, and responding to the increasing demand for a diversity of products that are eco-friendly. One such example is ‘fish-friendly’ rice produced from irrigated, rainfed and deepwater rice ecosystems, which values the diversity of aquatic species and their importance for rural livelihoods.