The paper presents the feedback of the project leaders on the management of interdisciplinarity within 14 scientific projects (3 networks and 11 research projects) carried out as part of a program on the integrated management of animal health, as well as the feedback of researchers involved in the overal management of the program. The difficulties encountered by the project leaders are related to the need for acculturation among disciplines, to the equilibrium and mutual respect between disciplines within the project, to the lack of time dedicated to the scientific animation of the project, and to the difficulty of publishing interdisciplinary work. The level of interdisciplinarity varies among projects, from the juxtaposition of several disciplines, up to a true integration of them. Recommendations are proposed to future project leaders at the various steps of a projet, that are the co-design step, in order to facilitate the de-centering of disciplinary questioning, the implementation step of the project, with an agile management, and the report step, in order to analyse how interdisciplinarity has moved disciplinary lines and modified initial questions. Strengthening of interdisciplinary programs should favor training researchers to interdisciplinarity, provide support for the conception of interdisciplinary projects, and analyse to wich degree the integration of disciplines was achieved in the projects.