The need for better conciliation between food production and environmental protection calls for new conceptual approaches in agronomy. Ecological intensification (EI) is one of the most encouraging and successful conceptual frameworks for designing more sustainable agricultural systems, though relying upon semantic ambivalences and epistemic tensions. This article discusses abilities and limits of the EI framework in the context of strong social and environmental pressure for agricultural transition. The purpose is thus to put EI at stake in the light of the results of an interdisciplinary and participatory research project that explicitly adopted EI goals in livestock semi-industrialized farming systems. Is it possible to maintain livestock production systems that are simultaneously productive, sustainable, and viable and have low nitrate emissions in vulnerable coastal areas? If so, how do local stakeholders use these approaches? The main steps of the innovation process are described. The effects of political and social dynamics on the continuity of the transition process are analyzed, with a reflexive approach. This experiment invites one to consider that making EI operational in a context of socio-technical transition toward agroecology represents system innovation, requiring on-going dialogue, reflexivity, and long-term involvement by researchers.