Participatory and transdisciplinary approaches to research, modeling, and community engagement have become increasingly popular. Yet even when diverse stakeholders and scientists are brought together, it is not clear they share the same understandings of the goals of the participatory process or how stakeholder knowledge will be utilized. Our research documents the degree of alignment in initial expectations between stakeholders and scientists in a large participatory modeling project designed to determine how changes in global trade will impact food-energy-water systems in the eastern Corn Belt/Great Lakes region of the USA. We combined qualitative semi-structured interviews and a quantitative online survey to measure how consistent the expectations and understandings were between scientists and stakeholder advisors at an early stage of the project.We found that people participated for many personal and professional reasons. All participants were seeking an opportunity to engage in stimulating and enlightening discussions. Although the project was conceived using a co-production model, most participants initially assumed that stakeholder roles would be consultative, where stakeholder input would be used to inform decisions by scientists about scenario and model choices. Although everyone valued scientific and societal outcomes, scientists prioritized academic outputs more highly than stakeholders, who pointed to the use and impact of the work outside of academia as the most important outcome. Overall, we identified areas of both alignment and misalignment in initial understandings and expectations among scientists and stakeholders that should be addressed through an adaptive process to maximize the likelihood of project success.