Stakeholders from academic, political or social spheres encourage the development of more sustainable forms of agriculture. Considering the scale and scope of the sustainability transition, it is challenging to the agricultural sector at large. The main question is how to support the transition process? In this communication, we expose how wicked problems related to the sustainability transition of farming systems can be addressed by agricultural science to better understand and support transition processes. We elaborate on the potential for articulation of three research approaches: comprehensive analysis, co-design and simulation modelling that refer to different stances and methodological choices. Comprehensive analysis of the sustainability transition of farming systems provides historical or snapshot perspectives on agricultural and institutional contexts and on the interplay between on one hand, the resources, their management and related performances of farming systems and on the other hand technical, economic and sociocultural dimensions of change. Co-design of the sustainability transition of farming systems stimulates local-scale experiments of transitions in the real world and the identification of alternatives for change from the farming system level to the territorial level. Simulation modelling consists of explorations of scenarios of management at different levels and assessment of their impacts. It offers a future-oriented perspective on transitions. We illustrate this potential for articulation of research approaches by taking the case of two examples of research conducted in our multidisciplinary research group applying to agricultural water management and autonomy in crop-livestock systems. The resulting conceptual framework is the first proposed to organize research to better understand and support sustainability transitions in the agricultural sector.