While research and innovation (R&I) are at the core of the response to the pandemic itself in the areas of virology, vaccines development, treatments and diagnostics, it will be crucial also in the economic recovery from the crisis, not only to spur economic activity, but also to accelerate the transitions that our planet and society need. Hence this working paper discusses the role of R&I in the short-term context of the sanitary crisis and economic contraction, as well as in the longer term and aftermath of the crisis, as a key driver of the recovery. It concludes that policy should promote the coordination of the R&I response to COVID-19, support businesses to cope with the crisis and create innovative solutions to tackle the direct and indirect consequences of the pandemic, help workers and businesses adjust to new ways of working and operating, and build system-wide resilience to address long-term threats such as climate change.