Health rights of prisoners has long been a neglected political issue in Africa, where over one million people are detained, and almost half of whom are in pre-trial detention. African prisons constitute high-risk environments for communicable disease transmission. During the COVID-19 pandemic, the public health literature on African prison responses focused on preparedness as it related to testing capacity, quarantine practices and personal protective measures to mitigate disease spread. This article combines the right to health as narrowly defined by a prisoner’s right to access non-discriminatory equivalent health care, with a broader focus on assessing normative standards of detention. A comparative legal realist assessment of prison operations in South Africa, Malawi and Zimbabwe during COVID-19 state disaster measures is presented, focusing on the environmental determinants of health (ventilation, minimum floor space, water, sanitation, hygiene and nutrition) in prisons. It reveals the inherent tensions in ensuring a balance between respecting the fundamental rights of people living and working in prisons, ensuring adequate environmental health standards and mitigating disease during public health emergencies. Despite insufficient government resourcing and inadequate coverage of COVID-19 responses, few severe outbreaks were reported. This could be due to lack of testing, reporting or other factors (asymptomatic infection, acquired immunity). Prison congestion and unrest however affected prisoners and staff fearful of hazardous living and occupational health conditions. COVID-19 as public health emergency amplifies the need to address systemic deficits in infrastructure, resourcing and efficiency of criminal justice systems. Policy level and pragmatic recommendations for enhanced human rights practice are outlined.