Agriculture provides food to a still growing population but is a major driver of the acceleration of global nutrient flows, climate change, and biodiversity loss. Policies such as the European Farm2Fork strategy aim to mitigate the environmental impact of land-use by fostering organic farming. To assess long-term environmental impact of organic food production we synthesized more than four decades of research on agronomic and environmental performance of the oldest system comparison experiment on organic and conventional cropping systems (DOK experiment). Two organic systems (bioorganic and biodynamic) are compared with two conventional (manure-based integrated and mineral-based) systems all with the same arable crop rotation including grass-clover, and manure from livestock integrated in all except the mineral-based system. Organic systems used 92% less pesticides and 76% less mineral nitrogen than conventional systems. Nitrogen use efficiency, that also considers biological nitrogen fixation, was above 85% for all systems. Organic fertilization with farmyard manure maintained or increased soil carbon and nitrogen stocks in the long term, especially in the biodynamic system with manure compost. Conventional mineral-based cropping reduced soil organic carbon and nitrogen stocks. Higher soil organic carbon stocks in organic cropping did not translate to increased N2O emissions, which were the main driver for 56% lower soil-based, area-scaled climate impact compared to the integrated conventional system with manure. Organic cropping systems, especially compost-based biodynamic, showed enhanced soil health, richness of micro- and macrofauna and weed species. Highest yields were achieved in integrated conventional system, with highest total nitrogen inputs and enhanced soil health compared to pure mineral fertilization. Yet, these benefits come at the cost of lower nitrogen use efficiency and higher N2O emissions. Despite a rigorous reduction of inputs yields of the organic systems achieved 85% of the conventional systems. We demonstrate at field level that organic cropping systems with reduced external nutrient inputs have less climate impact and a larger in-situ biodiversity, while providing a fertile ground for the future development of sustainable agricultural production systems.