Introduction Discrimination and structural violence experienced by sexual and gender minorities are the source of social inequalities in health. The last decade has been marked by major developments in the provision of sexual health services for these minorities in France. This paper presents the research protocol of the Services for Minorities-Lesbian Gays Bisexuals Transgender Intersex+ (SeSAM-LGBTI+) study, which aims to document the health, social and professional challenges in the organisation of current health services for sexual and gender minorities in France. Methods and analysis The SeSAM-LGBTI+ study relies on a multidisciplinary qualitative study. It has two objectives: (1) to analyse the history of the development of LGBTI+ health services in France, through interviews with key informants and rights activists and through a study of archives and (2) to study the functioning and challenges of a sample of health services currently offered to LGBTI+ people in France, through a multiple case study, using a multilevel and multisited ethnography. The study will rely on approximately 100 interviews. The analysis will be based on an inductive and iterative approach, combining sociohistorical data and the cross-sectional analysis of the case studies. Ethics and dissemination The study protocol has undergone a peer review by the Institut de Recherche En santé Publique’s scientific committee and has been approved by the research ethical committee of Aix-Marseille University (registration number: 2022-05-12-010). The project has received funding from December 2021 to November 2024. The results of the research will be disseminated from 2023 onwards to researchers, health professionals and community health organisations.