This paper considers how ecosystem-based research projects can be managed for a successful deployment of systemic and disruptive innovation. Such projects are defined as assignments in which heterogeneous organisations must invest upfront, aiming at co-constructing a systemic offer with shared interest, shared uncertainty and high economic, environmental and social impacts. Innovation management, ecosystem, and public-private partnership literatures have been investigated, as well as two European Commission funded research projects aimed at smart mobility infrastructure development. Results show these projects are both critical and disappointing for each player. We explain this contradiction of value perception showing that partners need such ecosystem projects to go forward and update their competences and roadmaps, but that the observed project management approach hampers the collectively built learning and the evolution of the strategic agenda of each partner. In conclusion, we define the concept of proto-ecosystem as an intermediary 'management object' for innovation management, and point out implications to manage such projects in order to unfold their whole potential.