Varietal and genetic diversity sustain modern agriculture and is provided by breeding systems. Failures in these systems may cause insufficient responses to plant diseases, which threatens food security. To avoid these failures, an understanding of the governance challenges in providing varietal and genetic diversity is required. Previous studies acknowledge the complexity of seed breeding, framing the discussion in terms of rivalry and excludability. We consider breeding systems as social-ecological systems that focus on activities that generate varietal and genetic diversity and their adaptive ability. We use an inductive approach based on qualitative methods combined with the social-ecological system framework (SESF) to depict how highly context-dependent German winter wheat breeding, multiplication, and farming activities are. Our results show that the challenges for governance lie in providing credible and symmetric information on variety performance to all actors. This is the means to steer actors into collective action by subcontracting, buying, or saving seed. Based on our application of the SESF to the German wheat breeding system, we propose to develop a more general, sectoral SESF for the sustainable governance of plant breeding by offering an adaptable template for analyses of seed systems in other contexts.