Like conventional farming, organic agriculture in the Netherlands is highly specialized. Both livestock and arable farmers have optimised production independent of each other which has led to a high use of external inputs from conventional agriculture (manure and other fertilisers and straw) and feedstuffs (mainly concentrate feed) from abroad. This situation conflicts with important principles of organic agriculture such as a balance between livestock and arable farming, closing nutrient cycles and regionally based production. In an attempt to find solutions for this dilemma, the Louis Bolk Institute (LBI) started with a series of projects called “Partner Farms” in which the LBI cooperated closely with leading edge farmers (Wit et al, 2003). In these projects the cooperation between specialised livestock and arable farmers was stimulated, in some cases ultimately leading to “mixed farms at a distance”. Later the LBI became involved in a combined research programme together with various research institutes of the Wageningen University and Research aimed at studying “intersectoral cooperation” and nutrient cycles on a national level, using both modelling and participatory research (Enting et al. 2005). In both cases it became clear that the simultaneous use of both types of research methodology is necessary to get credible and practically viable results