Agriculture must face a number of very pressing environmental issues. We used the prototyping method to design three innovative cropping systems, each satisfying three ambitious goals simultaneously: (1) overcoming a major environmental constraint, which represents a major break regarding objectives to be reached in current cropping systems (differing between systems: a ban on all pesticides but with chemical nitrogen (N) fertilizer permitted; reducing fossil energy consumption by 50%; or decreasing greenhouse gas (GHG) emissions by 50%), (2) meeting a wide range of environmental criteria and (3) maximizing yields, given the major constraint and environmental targets. A fourth cropping system was designed, in which the environmental and yield targets were achieved with no major constraint (the productive high environmental performance cropping system (PHEP) system). The performances of these innovative cropping systems were compared to a conventional system in the Ile-de-France region. We used a three-step prototyping method: (1) new cropping systems were designed on the basis of scientific and expert knowledge, (2) these system prototypes were assessed with tools and a model (ex ante assessment) adjusted to the set of constraints and targets, with optimization by an iterative process until the criteria were satisfied and (3) evaluation in a long-term field experiment (ex post assessment), which is currently underway. We describe only the first two steps here, together with the results of the prototypes assessment with tools and a model. The pesticide, energy and GHG constraints were fulfilled. All these innovative systems satisfied environmental criteria in terms of nitrogen and phosphorus management, pesticide use, energy consumption and crop diversity. For the pesticide-free system, the soil organic matter indicator was lower than expected due to frequent plowing (every 2 years) and yields were 20–50% lower than for the PHEP system, depending on the crop considered. We focus our discussions on the design methodology and the availability of scientific knowledge and tools for projects of this type.