"Achieving sufficient and stable crop yields with limited cropland and without excessive use of non-renewable resources under a changing climate are the multifunctional challenges of future agriculture. We compared the performance and sustainability of organic and conventional cropping systems in the DOK long-term systems comparison after 40 years of management. For the first time we present a comprehensive evaluation of the whole DOK design including the systems with reduced stocking rates. Yield, nutrient dynamic and soil quality evaluations show clearly the trade-offs between productivity and sustainability in organic as well as in conventional systems. Low input conventional systems reveal the best input-output performance but lowered soil quality; regular organic systems were most sustainable but achieved only moderate non-legume yields.