Background: During 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. Method: This 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 dissemination: Approval 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 number NCT06090006.