Background Virus Resistant Cassava for Africa (VIRCA) is an agricultural biotechnology public-private partnership (PPP) comprising the Donald Danforth Plant Sciences Center (DDPSC), National Agricultural Research Organization (NARO) of Uganda and Kenya Agricultural Research Institute (KARI). The project seeks to develop virus-resistant cassava for farmers in Kenya and Uganda. Yet, there is much public skepticism about the use of genetically modified (GM) crops and private sector involvement in Africa. This case study sought to understand the role of trust in the VIRCA partnership. Methods We conducted semi-structured, face-to-face interviews to obtain stakeholders’ views on the challenges to, and practices for, building trust in the VIRCA partnership. Interviewee responses, together with relevant documents and articles, were analyzed to generate descriptions of how trust is operationalized in this evolving agbiotech PPP. Data were analyzed based on recurring and emergent themes from the interviewee responses. Results Various factors undermine and build trust in agbiotech PPPs. Individual and institutional enthusiasm and detailed collaborative agreements stipulating partner roles and responsibilities are likely to enhance trust among partners. On the other hand, negative perceptions propagated by international partners about the capacities of African institutions and scientists, coupled with slow regulatory processes in Africa, are likely to be impediments to trust building. Conclusions Based on the findings of this study, we have derived four key lessons. First, differences in the capacity of the partner institutions and individuals should be respected. Second, technical and infrastructural capacity support for regulatory processes in Africa must be built. Third, detailed agreements and open and transparent partner practices during project implementation are necessary to dispel perceptions of inequality among partners. Fourth, institutional and individual commitment to succeed is important in initiation of the project. These lessons can be used by other agbiotech PPPs as a guide for building trust among partners and with the community.