African higher education institutions face severe funding shortages and pressure to align with market demands, leading to the rise of public-private partnerships (PPPs) as alternative solutions. While PPPs can mobilize resources and foster innovation, they raise critical concerns regarding academic freedom, institutional autonomy, and equitable access. This study employs a qualitative comparative case study based on secondary data from policy documents, institutional reports, and academic literature. Three national contexts are analyzed: Morocco’s resource-backed model at Mohammed VI Polytechnic University (UM6P), South Africa’s structured legal framework, and Uganda’s market-driven approach. Findings reveal that well-regulated PPPs, as in Morocco and South Africa, strengthen infrastructure and research capacity while safeguarding academic freedom. In contrast, Uganda’s weaker governance context shows heightened commercial pressures, restricted autonomy, and greater inequities. The study concludes that PPPs in Africa represent a double-edged sword, with their success contingent on governance frameworks that protect academic freedom alongside efficiency.