Temperatures across Africa are expected to rise at up to twice the rate of mean global temperatures, posing significant health threats to vulnerable communities. Prolonged exposure to high day- and night-time temperatures has been implicated in a myriad of adverse health outcomes. The built environment and inadequate housing can exacerbate these consequences, prompting the need to evaluate heat adaptation interventions as a sustainable adaptation strategy for low-income and informal settlement dwellers. The Heat Adaptation Benefits for Vulnerable groups In Africa (HABVIA) study aims to assess the impact of passive cooling interventions in homes on several key physiologic and mental health outcomes, as well as building internal thermal conditions. HABVIA is a 3-year prospective controlled study to identify, implement and assess heat adaptation solutions in four low-income communities in one urban and one rural site in Ghana and South Africa, respectively. In each site, N=240 participants (N=60 per site) will be assigned to intervention or control groups. The intervention is focused on lowering the nighttime temperature of the home environment. Health and biometric data will be collected through a combination of physiological measurements, questionnaires, and biochemical measures taken at 3 time points during the hot season. Clinical outcomes include objective sleep behaviour, core body temperature, physical activity, blood pressure, blood glucose, anthropometrics, and body composition. Indoor and outdoor environmental data will be collected continuously using fixed indoor sensors and automatic weather stations. Housing and community characteristics, and socio-economic information will be collected. Quantitative comparisons will be made between intervention and control conditions using generalised linear mixed models. Qualitative data from consultive workshops will be used to assess the acceptability and feasibility of the adaptations. Robust evaluation of the environmental and health outcomes of heat adaptations are limited for Africa, despite high climate vulnerability. HABVIA will address some of these gaps by assessing low-cost passive cooling interventions to promote heat resilience and improve health outcomes, providing real-world evidence for the feasibility of readily implementable and scalable adaptations in local contexts. Pan African Clinical Trials Registry (PACTR) PACTR202401521630856, version 1. Retrospectively registered on January 12, 2024.