There has been a rapid rise in the number of Mozambican universities in the past two decades, but corruption risks in these institutions and the research sector more broadly remains an under-examined area. Identified risks include political manipulation of university affairs by government, mismanagement of research grant funds and a lack of independence of the country’s quality assurance body. There are also reports of other forms of corruption such as bribery, plagiarism, academic fraud and sextortion for grades within universities. Several mitigation measures can be put into place to strengthen the integrity of the system, and these include accountability mechanisms within universities and research institutions, independence and increased capacity of the CNAQ, anti-plagiarism policies and tools, sanctions for academic dishonesty, anti-corruption clauses in research grant agreements, compliance assessments of universities and research institutions, and enhanced whistleblower protection.