Accomplishing and implementing sustainable development goals in the context of insular socio-ecological systems requires effective policy integration—i.e., the integration of policy actors across multiple sectors and levels of government to improve policy outcomes. However, achieving policy integration entails significant challenges because it is highly context-dependent. This study investigates policy integration within the complex socio-ecological context of the Galápagos Islands in Ecuador. The paper analyses Galápagos legal and planning documents to evaluate the extent to which they support comprehensive policy integration. The analysis found that recently adopted institutional arrangements have strengthened government institutions at the provincial level, and started to consider concepts relating to socio-ecological and land–sea management. Nevertheless, key policy actors and pressing issues remain unattended, due to policy inconsistencies, institutional arrangements limitations, and fragmented approaches to conservation and development control between provincial and local governments. Insights are presented to improve the comprehensiveness of policy integration in Galápagos based on a landscape-scale planning approach.