Little is known about the outcomes of in-school comprehensive sexuality education (CSE) programmes two or more years after programme completion, particularly in low-income countries. "Projet Jeune Leader," a youth-founded Malagasy organisation, conducted a retrospective, qualitative evaluation of a CSE programme in Madagascar. The objective was to explore how former participants assessed the programme's influence on their behaviours and lives. Our team conducted in-depth interviews with 34 young people (16-24 years old) who had participated in the programme when they were in middle school. We then synthesised the data using qualitative thematic analysis. Most interviewees indicated that the CSE programme positively contributed to some aspect of their transition to adulthood. Some reported safer sex practices, refraining from drug and alcohol use, and pregnancy prevention, while others reported improved relationships, and acts of leadership. While it is not clear which elements of the programme facilitated these changes, participants made recurrent references to relatable CSE educators and engaging pedagogy in their responses. These results encourage further research on the multi-faceted, and in some cases, non-health-related, outcomes of in-school CSE programmes in low-income countries. The work also provides critical youth-driven insights into CSE programme design to guide future programme planning and evaluation efforts.