Background Maize is the most important staple food in Kenya; any reduction in production and yield therefore often becomes a national food security concern. To address the challenge posed by the maize stem borer, the Insect Resistant Maize for Africa (IRMA) agricultural biotechnology public-private partnership (PPP) project was launched in 1999. There were, however, pre-existing concerns regarding the use of genetic engineering in crop production and skepticism about private sector involvement. The purpose of this case study was to understand the role of trust in the IRMA partnership by identifying the challenges to, and practices for, building trust in the project. Methods Data were collected by conducting face-to-face, semi-structured interviews; reviewing publicly available project documents; and direct observations. The data were analyzed to generate recurring and emergent themes on how trust is understood and built among the partners in the IRMA project and between the project and the community. Results Clear and continued communication with stakeholders is of paramount importance to building trust, especially regarding competition among partners about project management positions; a lack of clarity on ownership of intellectual property rights (IPRs); and the influence of anti-genetic modification (GM) organizations. Awareness creation about IRMA’s anticipated products raised the end users’ expectations, which were unfulfilled due to failure to deliver Bacillus thuringiensis (Bt)-based products, thereby leading to diminished trust between the project and the community. Conclusions Four key issues have been identified from the results of the study. First, the inability to deliver the intended products to the end user diminished stakeholders’ trust and interest in the project. Second, full and honest disclosure of information by partners when entering into project agreements is crucial to ensuring progress in a project. Third, engaging stakeholders and creating awareness immediately at the project’s inception contributes to trust building. Fourth, public sector goodwill combined with private sector technology and skills are necessary for a successful partnership. These findings may serve as a useful guide for building and fostering trust among partners in other agbiotech PPPs in sub-Saharan Africa.