BackgroundDuring adolescence, behaviours are initiated that will have substantial impacts on the individual’s short-term and long-term health and well-being. However, adolescents rarely have regular contact with health services, and available services are not always appropriate for their needs. We co-developed with adolescents a health and well-being check-up programme (Y-Check). This paper describes the methods to evaluate the feasibility, acceptability, short-term effects and cost-effectiveness of Y-Check in three African cities.MethodThis is a multi-country prospective intervention study, with a mixed-method process evaluation. The intervention involves screening, on-the-spot care and referral of adolescents through health and well-being check-up visits. In each city, 2000 adolescents will be recruited in schools or community venues. Adolescents will be followed-up at 4 months. The study will assess the effects of Y-Check on knowledge and behaviours, as well as clinical outcomes and costs. Process and economic evaluations will investigate acceptability, feasibility, uptake, fidelity and cost effectiveness.Ethics and disseminationApproval has been received from the WHO (WHO/ERC Protocol ID Number ERC.0003778); Ghana Health Service (Protocol ID Number GHS-ERC: 027/07/22), the United Republic of Tanzania National Institute for Medical Research (Clearance No. NIMR/HQ/R.8a/Vol.IX/4199), the Medical Research Council of Zimbabwe (Approval Number MRCZ/A/2766) and the LSHTM (Approval Numbers 26 395 and 28312). Consent and disclosure are addressed in the paper. Results will be published in three country-specific peer-reviewed journal publications, and one multicountry publication; and disseminated through videos, briefs and webinars. Data will be placed into an open access repository. Data will be deidentified and anonymised.Trial registration numberNCT06090006.