Fuzzy cognitive mapping (FCM) is an increasingly popular participatory modeling method that facilitates the creation of structured causal maps to compare perspectives on a particular social-ecological system among individuals or groups, as well as the analysis of perceived system dynamics and feedback loops. This chapter explores the value of FCM for understanding and/or improving institutions and institutional change, while highlighting trade-offs in study design and epistemological challenges related to stakeholder participation and modeling that may affect its efficacy for institutional analysis. Reflecting on the participatory challenges encountered during the application of FCM in a case study on Harmful Algal Blooms in coastal Peru, we emphasize the importance of acknowledging and addressing epistemological, theoretical tensions and power issues linked to FCM from the outset of the research process. This not only helps in navigating challenges throughout the process but can also promote more realistic expectations of the tool’s participatory potential. Finally, this chapter provides recommendations for researchers and practitioners that intend to use FCM in the realm of institutional analysis.