In this article we take inspiration from the experience of the JESSICA Initiative to delineate the rationale for a city-based, bottom-up approach to stimulate the economic recovery of the European Union. The proposed approach involves an agenda for a European research programme on urban management and finance, which brings together the vision of the city as a system of interlinked assets to be managed in a sustainable way and the use, in this context, of a methodology broadly inspired to corporate finance principles. The proposed agenda is intended to lead to better diagnostics and strategic investing to address urban transformation patterns likely to characterise the European city system in the coming years. This agenda should stimulate European researchers and practitioners to develop a methodology leading to the definition of sustainable productivity metrics for urban systems, as well as practical modelling strategies that can assist the decisions of city managers and long-term investors in urban infrastructure.