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Makerere University is the oldest and most prestigious university in East Africa. As one of the best universities on the African content, Makerere is aligned to three main activities; Teaching, Research, and Community Outreach, and these are inclined to 5 core values; allegiance to the institution, integrity, customer responsiveness, professionalism, and openness to diversity. Makerere University has a library system, hosting both electronic and print resources. The digitization of print resources has created a system, through which delicate material is conserved. The files and their metadata, using Dublin Core, are stored in the institutional repository and in the integrated library system (Virtua). The library system further generates library usage data which can be used in making acquisitions decisions. For most research output files, the data is available and would be archived alongside the digital files. Other than the National Biodiversity Data Bank which is transitioning to online, the rest of the data remains stored on authors’ personal computers and other storage tools. With support from the government and other development partners, Makerere university strives for a shift from a more academic-driven to a research-led university. This calls for more support from the university administration and other key units, to provide access points to linked data. This paper aimed at establishing the status of linked data at Makerere university, challenges encountered in data management, and prospect strategies. The researcher used an exploratory research methodology to generate key findings, from existing literature and personal experiences from experts. The findings reveal that Makerere university researchers archive their data in external repositories and that, while the Makerere Institutional Repository has the potential to host linked data, this service has not been exploited basically due to lack of skilled labor force, awareness, financial resources, and policy. However, this service, when incorporated in the institutional research agenda, can be implemented and also enhance data linking in the NBDB. It is anticipated that the results from this study will guide Makerere and other institutions in Uganda to embrace the value of linked data and therefore ignite its implementation.