Background Nigeria, Africa’s most populous country, has been the world’s largest cowpea importer since 2004. The country is currently in the early phases of confined field trials for two genetically modified crops: Bacillus thuringiensis (Bt) cowpea and nutritionally enhanced cassava (“BioCassava Plus”). Using the bio-safety guidelines process as a backdrop, we evaluate the role of trust in the operation of the Cowpea Productivity Improvement Project, which is an international agricultural biotechnology public-private partnership (PPP) aimed at providing pest-resistant cowpea varieties to Nigerian farmers. Methods We reviewed the published literature and collected data through direct observations and semi-structured, face-to-face interviews. Data were analyzed based on emergent themes to create a comprehensive narrative on how trust is understood and built among the partners and with the community. Results Our findings highlight the importance of respecting mandates and eliminating conflicts of interest; holding community engagement initiatives early on; having on-going internal discussion and planning; and serving a locally-defined need. These four lessons could prove helpful to other agricultural biotechnology initiatives in which partners may face similar trust-related challenges. Conclusions Overcoming challenges to building trust requires concerted effort throughout all stages of project implementation. Currently, plans are being made to backcross the cowpea strain into a local variety in Nigeria. The development and adoption of the Bt cowpea seed hinges on the adoption of a National Biosafety Law in Nigeria. For countries that have decided to adopt biotech crops, the Nigerian cowpea experiment can be used as a model for other West African nations, and is actually applied as such in Ghana and Burkina Faso, interested in developing a Bt cowpea.