Background In 1999, South Africa became the first African country to approve commercial production of subsistence genetically modified (GM) maize. The introduction of GM crop technology is often met with skepticism by stakeholders including farmers. The involvement of the private sector in this process can further breed mistrust or misperceptions. To examine these issues more closely, the objective of this case study was to understand the role of trust in the public-private partnership (PPP) arrangement involved in the development of Bacillus thuringiensis (Bt) maize in South Africa. Methods We conducted semi-structured, face-to-face interviews to obtain stakeholders’ understanding of trust in general as well as in the context of agricultural biotechnology (agbiotech) PPPs. A thematic analysis of the interview transcripts, documents, reports and research articles was conducted to generate insights into the challenges to, and practices for, building trust among the partners and with the public. Results The findings of this study are organized into four main lessons on trust building. First, as the end users of GM technology, farmers must be engaged from the start of the project through field demonstrations and educational activities. Second, an effective technology (i.e., the seed) is key to the success of an agbiotech PPP. Third, open communication and full disclosure between private sector companies and government regulatory bodies will build trust and facilitate the regulatory processes. Fourth, enforcing good agronomic practices, including appropriate management of the refuge areas, will serve the interests of both the farmers and the seed companies. Conclusions Trust has proven to be a critical factor determining the success of the Bt maize project in South Africa. Distrust of the private sector and of GM technology were cited as major barriers to building trust. The trust-building practices described in this case study have often served to overcome these barriers; however, erosion of trust was also present. The success of the project has been, and will continue to be, dependent upon the concerted effort of the farmers, government, and private sector players in the establishment and maintenance of trust.