Prosper Ngabonziza is actively involved in the The African Light Source (AfLS) project, as the Deputy Chair of the Executive Committee of the African light source foundation. AfLS project is working towards building a synchrotron light source on the African continent that will contribute significantly to the African science renaissance. For details on this project, see AfLS foundation website.
In June 2019, he has been nominated as a Fellow to the Rwanda Academy of Science.
Furthermore, he has been selected for a membership in the Global Young Academy for a period of 5 years beginning in June 2020. He served on the 2021/2022 Global Young Academy Executive Committee; and currently, he is serving as a Co-Chair of the Global Young Academy.