Multifunctional agriculture holds several potentials for applying new technologies and innovative processes to reduce its environmental impact in line with the European Green Deal. Though, new cooperation concepts are a sufficient tool to enhance these potentials, using interdisciplinary and cross-border approaches. Hence, Regional Innovation Strategies on Smart Specialization (RIS3) can play a key role on political level to foster regional innovation development on agriculture in rural areas. By analysing Smart Specialization priority areas, potential crossovers between this innovation policy and actual implementation in practice can be deduced for cross-border cooperation approaches. Thus, the conducted research offers a comparison of priorities for German regions involved into the RUBIN program as use cases, supporting rural and less developed regions. Through these introduced use cases and strategy analysis, the inductive and deductive research offers a cross-border cooperation concept for legume food production, exploiting spillover effects to other priorities related to multifunctional agriculture. The core element of the concept is the introduction of knowledge hubs with an interdisciplinary view to enhance and apply innovation potentials in line with RIS3, which create positive effects on the environmental impact from the start with legume as raw materials until an improvement of its product portfolio for consumption at the end.