IntroductionThe prevalence of chronic, lifestyle-related diseases is increasing among adults and children from low-income and middle-income countries. Despite the effectiveness of community-based interventions to address this situation, the benefits thereof may disappear in the long term, due to a lack of maintenance, especially among disadvantaged and high-risk populations. The KaziBantu randomised controlled trial conducted in 2019 consisted of two school-based health interventions, KaziKidz and KaziHealth. This study will evaluate the long-term effectiveness and sustainability of these interventions in promoting positive lifestyle changes among children and educators in disadvantaged schools in Nelson Mandela Bay, South Africa, in the context of the COVID-19 pandemic.Methods and analysisThis study has an observational, longitudinal, mixed-methods design. It will follow up educators and children from the KaziBantu study. All 160 educators enrolled in KaziHealth will be invited to participate, while the study will focus on 361 KaziKidz children (aged 10–16 years) identified as having an increased risk for non-communicable diseases. Data collection will take place 1.5 and 2 years postintervention and includes quantitative and qualitative methods, such as anthropometric measurements, clinical assessments, questionnaires, interviews and focus group discussions. Analyses will encompass: prevalence of health parameters; descriptive frequencies of self-reported health behaviours and quality of life; the longitudinal association of these; extent of implementation; personal experiences with the programmes and an impact analysis based on the Reach, Efficacy, Adoption, Implementation, Maintenance framework.DiscussionIn settings where resources are scarce, sustainable and effective prevention programmes are needed. The purpose of this protocol is to outline the design of a study to evaluate KaziKidz and KaziHealth under real-world conditions in terms of effectiveness, being long-lasting and becoming institutionalised. We hypothesise that a mixed-methods approach will increase understanding of the interventions’ capacity to lead to sustainable favourable health outcomes amid challenging environments, thereby generating evidence for policy.Trial registration numberISRCTN15648510