<p>The adoption of System Dynamic Modeling methodology for understanding complex environmental systems has increased significantly in recent years due to its ability to capture the dynamic behavior of a complex system over time. This study integrates participatory Causal-Loop Diagrams to map causal interrelations between key variables impacting the Galapagos Islands’ unique ecosystem into a quantitative System Dynamic Modeling to analyze the efficacy of various decarbonization strategies within tourism-centric island economies. The model evaluates anthropogenic emissions and simulates the period from 2019 to 2100 to understand the behavior of variables over time, factoring in historical data and the COVID-19 pandemic. Results indicate a delicate balance in tourism management, with accelerated growth leading to an “overshoot and collapse” dynamic, where long-term environmental degradation offsets initial economic benefits. Policies focusing on electrifying transportation and scaling up renewable energy can noticeably reduce air emissions, serving as a critical step towards the Galapagos’ transition to a low-carbon future. However, challenges persist due to the energy capacity gap. These findings highlight the complex interaction between tourism, population growth, emissions, and socio-economic well-being in island ecosystems that heavily rely on tourism for their economy. They provide a foundation for decision-makers that can be applied to other Small Island Developing States.</p>