Doctoral supervision has been described as a process, where research, knowledge and individuals are intertwined in a transformative process of a bidirectional nature, for both the student and his/her supervisor(s) (Halse, 2011; Kobayashi, 2014). This process relies on a human-centered system based on a dialogic and interactive relationship between two persons, their individualities and styles (Gatfield and Alpert, 2002), mixing power relations (Manathunga, 2007; Hemer, 2012), academic competences and inter/intra-personal spheres (Baptista, 2015). However, research educational efforts are usually split into programmes focused either on the doctoral candidates, putting the emphasis on the development of the research student, or more recently, on the supervisors with a range of initiatives in supervisor development (Lee, 2015). As a result, they still miss the “supervision system”. We present EDEN1, a training programme for the supervisory dyad in which the doctoral candidate and his/her supervisor(s) are educated together as a continuously learning system. After presenting the evolving French context of PhD and INRA2 in which EDEN has been designed, we develop our viewpoint of the PhD process as a professionalisation and peer-learning process relying on a mentoring relationship that aims at developing the scientific autonomy for the young researcher. We then detail our educational choices, i.e. enhancing reflexivity through action learning, combining inputs and practice sharing, highlighting doctoral diversity and scientific pluralism. We also describe the one-week organisation of EDEN courses, with plenary sessions, workshops in small groups, specific sessions either for students or supervisors and working sessions for the dyads. To conclude, we highlight some questions that emerge from the EDEN experience after 3 years of implementation, thus outlining some possible developments for the EDEN programme as well as research questions in educational research.