This article argues that educational research in Uganda is facing severe glitches, such as low research capacity. Most private universities seem to be more focused on their day-to-day survival than identifying their research-specific needs and engaging in quality research activities. Issues of research capacity-building remain a major concern amid a lack of resources and institutional environments in which academics work. Capacity-building and research engagements would help to strengthen strategic planning and influencing policy. Hence, this study fills this gap. Specifically, it explores the perceptions and experiences of academic staff regarding research capacity-building. The study identifies the challenges that hamper educational research and capacity-building opportunities associated with the development of research capacities as perceived by a sample of staff members in the identified institutions. To achieve this objective, a qualitative research design was adopted using focus group interviews to collect data from a sample of staff. In total, 12 focus group discussions were conducted with between 8–10 persons per group. Rank ordering of responses on specific issues was done during data analysis. The findings showed that the major factors responsible for low research output include capacity-building gaps, lack of financial resources, difficulty in identifying specific calls for abstracts and manuscripts, work overload for faculty staff, limited research writing skills, and bad experiences during previous research engagements, as presented and discussed below. Based on the findings, we make the following recommendations. First, the government should earmark a significant amount in the national budget for research and innovation that institutions in Uganda can easily access, including private academic institutions. Second, institutions should continuously engage their staff regarding research and improve their research capacity through training, workshops and symposiums.