In this paper, bioethanol and fruit processing clusters in Uganda were taken as sectoral innovation systems, and enabling conditions and barriers to their growth were analysed from a technoscientific and innovation systems perspective. Active participation of entrepreneurial university scientists in the clustering process appears to be an enabling factor. Absence of goals and incentives specifically to attract investments in the cluster areas and to drive formation of markets for cluster products is a major barrier. Adopting more inclusive innovation policies, and having in place good community engagement strategies, could help overcome the barriers and expand opportunities for clusters in low resource settings to grow and become competitive.