Public universities in Uganda are increasingly recognised as drivers of innovation and student entrepreneurship, aligned with Vision 2040, NDP IV, and the Sustainable Development Goals (SDGs). Innovation hubs within these institutions are established to incubate student-led start-ups. However, access to finance, weak marketing strategies, and fragmented institutional support continue to hinder their performance. This study investigates how integrated marketing and financial models can enhance the effectiveness of innovation ecosystems in Uganda’s public higher institutions of education (HEIs). It explores three research questions: (i) What financing strategies are employed by university-based innovation hubs? (ii) What marketing approaches do student-led start-ups utilise? (iii) Which institutional or policylevel enablers and constraints affect start-up success? A mixed-methods approach was used. Quantitative data was collected from structured surveys administered to 100 student-led startups across three public universities via simple random sampling. Qualitative data was collected via 25 semi-structured interviews and four focus group discussions with hub managers, student entrepreneurs, university administrators, government officials, and financial actors, selected through purposive sampling. Data was collected from 85 respondents across three public universities using a mixed-methods approach. Regression results revealed that financial model sustainability (β = 0.63, p < 0.05) significantly predicted innovation hub performance, while marketing strategies had a moderate but positive effect (β = 0.41, p < 0.05). The results show that successful start-ups often use inclusive financing options, such as seed grants, and employ context-specific marketing tools, such as digital branding. Hubs that provide mentorship, financial literacy, and market linkages significantly improve start-up growth and sustainability. Nevertheless, policy misalignment, limited scalability, and weak coordination remain key challenges. The study provides a practical framework for integrating marketing and financial strategies into HEI innovation management, offering policy insights for NCHE and university councils seeking to operationalise innovation and entrepreneurship within Uganda’s higher education system.