AbstractConcerns about the negative impacts of productivist agriculture have led to the emergence of two forms of ecological modernisation of agriculture. The first, efficiency-substitution agriculture, aims to improve input use efficiency and to minimise environmental impacts of modern farming systems. It is currently the dominant modernisation pathway. The second, biodiversity-based agriculture, aims to develop ecosystem services provided by biological diversity. It currently exists only as a niche. Here we review challenges of implementing biodiversity-based agriculture: managing, at the local level, a consistent transition within and among farming systems, supply chains and natural resource management. We discuss the strengths and weaknesses of existing conceptual frameworks developed to analyse farming, social-ecological and socio-technical systems. Then we present an integrative framework tailored for structuring analysis of agriculture from the perspective of developing a territorial biodiversity-based agriculture. In addition, we propose a participatory methodology to design this agroecological transition at the local level. This design methodology was developed to support a multi-stakeholder arena in analysing the current situation, identifying future exogenous changes and designing (1) targeted territorial biodiversity-based agriculture, (2) the pathway of the transition and (3) the required adaptive governance structures and management strategies. We conclude by analysing key challenges of designing such a complex transition, developing multi-actor and multi-domain approaches based on a combination of scientific and experiential knowledge and on building suitable boundary objects (computer-based and conceptual models, indicators, etc.) to assess innovative systems designed by stakeholders.