Current food production systems are major contributors to the environmental degradation that leads to climate change and biodiversity loss. Levels of production required for future food security cannot be met by further increases in inputs of non-renewable resources. The world's food crops must therefore be managed in a sustainable way that maintains long-term ecological functioning, including nutrient, carbon and water cycles, soil quality, primary productivity, microbe-plant associations, pest and pathogen regulation, pollination and arable food web resilience. All of these are determined by agronomic practices at local and regional scales, and all are sustained by the abundance, diversity and functional composition of plants, microbes and invertebrates in the farmed ecosystem. Presence of viable populations and communities of these organisms is therefore essential for system resilience. Long-term sustainability must rely more heavily on the internal generation of products and regulatory ecosystem services than on external inputs. Fully closed systems are impossible to achieve in agriculture as the product is removed for human consumption. There is ample evidence, however, that semi-closed, regenerative, systems can harness the ecosystem services provided by functional biodiversity to enhance crop production whilst simultaneously improving environmental quality. Here, agroecological alternatives to intensive farming practices are reviewed, focusing on key functional indicators and whole-system integration of practical management options designed to achieve multiple beneficial outcomes at field and farm scales.