The research and development (R & D) Framework Programmes (FPs) are the main tool for fostering research and technological development within the European Research Area. Given the high concentration of projects in few hubs, it is advisable to examine the impact of them on the regional innovation and scientific capabilities. The main aim of this study is to shed light on the effects of the 6th and 7th FPs on regional innovation and scientific performance. The comprehensive database of projects was built by the authors from the CORDIS dataset. The methodology is based on the ordinary least square and Tobit techniques. Empirical evidence highlights the role played by the coordination and the participation in projects to foster innovation and scientific outcomes. Likewise, coordination of projects is more effective in encouraging innovation in less developed regions than in the developed ones. The opposite applies to scientific publications. Current allocation criteria may maintain geographical inequalities.