Transformative change in primary food production is urgently needed in the face of climate change and biodiversity loss. Although there are a growing number of studies aimed at global policymaking, actual implementations require on-site deep analyses of social-ecological feasibility. Here, we report the first implementations of low-input mixed polyculture of highly diverse crops (synecoculture) in Japan and Burkina Faso. Results showed that the self-organized primary production of ecosystems follows a power law and performs better compared with conventional monoculture methods in 1) promoting diversity and total quantity of products along with rapid increase of in-field biodiversity, especially in a semi-arid environment where local reversal of regime shift is observed; 2) a fundamental reduction of inputs and environmental load; and 3) ecosystem-based autonomous adaptation of the crop portfolio to climatic variability. The overall benefits imply substantial possibilities for a new typology of sustainable farming based on human-guided augmentation of ecosystem services and biodiversity maintenance mechanisms that could overcome the historical trade-off between productivity and biodiversity.