To move today’s agricultural and urban systems towards tomorrow’s circular economy and respond to climate change, it is imperative to turn organic residues and wastewater into resourceful assets. This article discusses the changes that are needed in research to drive this paradigm shift and to go from a “losses and waste” situation to a “resource and opportunities” ambition. The current lines of research aim to maximise the use and value of biomass or organic residues and wastewater and propose new organisational schemes driven by technical innovations. Exploring the pathways to a sustainable future through many domains let us identify five challenges to structure the research efforts and find circular bioeconomy solutions for organic residues and wastewater: (1) proposing innovative processes and integrated multi-process systems; (2) promoting the emergence of multi-scale and cross-sectoral organisations; (3) developing multi-performance evaluation methods, (4) rethinking research–society intersections, and (5) enhancing research–legislation interactions. We end by outlining prospects for moving forward past current limitations: beyond increasing knowledge, research will continue its own transition. Our responsibility today is not to think about what we could do for a better world but what we should do to make our ever-changing world even better and more sustainable.