The recently described persistent ill health after acute COVID-19, so called “long COVID” has emerged as a major concern. We conducted a prioritisation exercise to identify research priorities for the long term effects of COVID-19 in airways diseases. A total of 202 international experts were invited to submit a minimum of three research ideas. Following a two-phase internal review process, a final list of 98 research questions was scored by 48 experts. The top ranked research question proposed investigating the relationship between an admission prognostic score and post-discharge morbidity at 3- and 12-months in groups of patients with and without pre-existing airways diseases. High scores were also assigned to comparing those two groups of patients in prevalence and severity of post-COVID-19 fatigue, sarcopenia, anxiety, depression and risk of future cardiovascular complications. Our approach has allowed development of a priority list that may inform future research studies and funding decisions. This prioritisation process can be adapted to other areas in long COVID.