In trying to respond to societal demands for sustainable development, farming systems worldwide face a range of environmental, technical and economic challenges. These challenges call for renewed methodologies that can be used to support farmers in designing innovative agricultural production systems at the farm level. This paper aims to analyze the various methods described in scientific literature. The review is based on the analysis of 80 reference papers published in international scientific journals between 1999 and 2010. We focused in particular on the purpose of the research, which fell into two broad categories: "design" and "design support". We also examined the use of models to represent production systems and to evaluate ex-ante the impact of innovations on these systems' functioning and performance. In so doing, we developed a classification system to organize the studies into five sub-categories according to the type of methodology followed, namely: prototyping and design modelling for design orientated studies; participation, support modelling and advisory for design-support orientated studies. We found that very few studies attempt to address the three main components of an innovation process in agricultural production systems (biotechnical processes, farm management, and advisory services) within a single research framework. We therefore developed such a framework by connecting the design and design support orientations together with biotechnical research and conducting integrated research both at farm and advisory service levels.