This study provides an in-depth assessment of Spain’s innovation system and the current state of knowledge transfer and collaboration. It identifies five priority areas for reform and long-term investment that should provide the basis of a new Roadmap. These include granting greater operational autonomy to universities and public research organisations in return for accountability on outcomes, putting in place a better integrated system of incentives that takes both individuals and organisations into account, and ensuring sustained investment in core capabilities to connect science and business. To put these reforms in motion and sustain them over time, a new type of covenant between science and society is needed in Spain today. This should be based on a ‘new deal’ between actors in the science and innovation system and society at large, committing to place the pursuit of concrete social benefits in return for more stable and predictable support.