Priority setting represents an even bigger challenge during public health emergencies than routine times. This is because such emergencies compete with routine programmes for the available health resources, strain health systems and shift health-care attention and resources towards containing the spread of the epidemic and treating those that fall seriously ill. This paper is part of a larger global study, the aim of which is to evaluate the degree to which national COVID-19 preparedness and response plans incorporated priority setting concepts. It provides important insights into what and how priority decisions were made in the context of a pandemic. Specifically, with a focus on a sample of 18 African countries’ pandemic plans, the paper aims to: (1) explore the degree to which the documented priority setting processes adhere to established quality indicators of effective priority setting and (2) examine if there is a relationship between the number of quality indicators present in the pandemic plans and the country’s economic context, health system and prior experiences with disease outbreaks. All the reviewed plans contained some aspects of expected priority setting processes but none of the national plans addressed all quality parameters. Most of the parameters were mentioned by less than 10 of the 18 country plans reviewed, and several plans identified one or two aspects of fair priority setting processes. Very few plans identified equity as a criterion for priority setting. Since the parameters are relevant to the quality of priority setting that is implemented during public health emergencies and most of the countries have pre-existing pandemic plans; it would be advisable that, for the future (if not already happening), countries consider priority setting as a critical part of their routine health emergency and disease outbreak plans. Such an approach would ensure that priority setting is integral to pandemic planning, response and recovery.