While innovation has emerged as an imperative, external pressures threaten to close down the space for innovation and experimentation. This chapter looks at how innovation efforts are organised in terms of resources, organisational contexts, dynamics as well as collaboration. It identifies how innovation could be better embedded and promoted in programming, financial and operational processes as well as in staff learning and development approaches. It discusses the role of innovation portfolios to enhance learning and oversight, and to underpin innovation governance and strategic decision-making. The chapter also analyses the tendency to ignore national and local actors and its consequences on the type of innovations that are funded – leading to more incremental innovations that maintain the status quo than transformative approaches that disrupt it.