Background <p>The increase in sharing of human biological materials and associated data in collaborative research underpins the need for robust regulatory frameworks. This study explored researchers’ perspectives on the use of material transfer agreements in biobanking research.</p> Methods <p>A qualitative descriptive study was conducted among researchers at two research institutions in Uganda. Fourteen researchers were purposively selected to participate in key informant interviews. Data were analysed using thematic analysis. NVivo 12 software was used to organize the data.</p> Results <p>Four themes were generated from the data: the importance of material transfer agreements, facilitators of successful development and execution of material transfer agreements, negotiating power dynamics between institutions in drafting of material transfer agreements, and barriers and challenges to the drafting and execution of material transfer agreements. Material transfer agreements were considered legal documents that describe the obligations of each party during the execution of the study. Researchers felt that robust ethical and legal frameworks, having multi-disciplinary teams and transparency were key to the successful development and execution of material transfer agreements. Researchers mentioned power dynamics, limited understanding and experiences with material transfer agreement processes, protracted bureaucratic approval processes, and differences in policies and laws across different jurisdictions as challenges to the drafting and execution of material transfer agreements.</p> Conclusion <p>The material transfer agreement is key to ensuring fairness in collaborative research, and the processes to ensure fairness in the drafting and execution of the material transfer agreement require empowerment of partners in resource-limited settings through effective regulatory frameworks and legal support to negotiate better.</p> Clinical trial number <p>not applicable.</p>