This study explores how an inclusive governance of “niche” innovations with family farmers enables or limits the realization of just transitions in family farming at different scales, from the local to the national levels. The research focuses on a case study in the Brunca region of Costa Rica, which has pioneered innovations for bean research with family farmers. The primary source of information for the study was in-depth interviews with relevant stakeholders. Secondary information comes from a desk review of the relevant policies and strategic documents from the relevant authorities. Lastly, a semi-scoping review was conducted to explore gender and intergenerational gaps in plant breeding, as well as potential conflicts between plant breeding and on-farm agro-diversity. The inclusive governance of bean research contributes to the realization of just-transition dimensions of justice, such as recognitional, procedural, and distributional justice, as a result of farmers’ engagement in participatory plant-breeding processes, and due to the coordination between different institutions at the local and national levels. Progress has been made in terms of the recognition and participation of farmers in research and in decision-making locally. The findings show interactions between the local and national scales, in terms of the commercialization of farmers’ seeds. However, the Costa Rican program for bean research struggles to engage family farmers in national decision-making processes and falls short of addressing equality and intergenerational issues. It also faces challenges in reaching a balance between short-term income generation and long-term conservation of agro-biodiversity on the farm. Fostering just transitions in family farming would require a greater inclusion of women and youth by the Costa Rican bean system. This implies allocating resources to increase their capacities and participation in bean research, as well as in decision-making at all levels. This is imperative and could be achieved if the government and relevant stakeholders align their strategic objectives and priorities to shorten gender and intergenerational gaps within the bean production system.