<![CDATA[Graphical Abstract Highlight Research 1. Ecotourism development in the Gili Matra Marine Protected Area was classified as moderately sustainable, but sustainability performance remained uneven across dimensions. 2. The institutional dimension showed the highest sustainability score, whereas the ecological dimension emerged as the principal limiting factor. 3. Leverage analysis identified coastal degradation, waste and pollution pressure, stakeholder coordination, and social conflict as the main priority attributes affecting sustainability. 4. Spatial conformity analysis revealed continued tourism and fisheries activities in zones intended for stronger protection, indicating incomplete zoning implementation. 5. Integrating RAPFISH-MDS with GIS-based zoning conformity analysis provided an operational framework for defining management priorities in small-island marine protected areas. Abstract Marine protected areas (MPAs) in small-island settings are expected to balance conservation objectives with tourism-based economic development. However, tourism growth within protected coastal systems may intensify ecological degradation, spatial-use competition, and social inequality when governance capacity, zoning compliance, and supporting infrastructure fail to keep pace with increasing visitor pressure. This study evaluated the sustainability of ecotourism development in the Gili Matra Marine Protected Area (MPA), Indonesia, by integrating multidimensional sustainability assessment with spatial conformity analysis. An integrated mixed-methods approach was applied using RAPFISH–Multi-Dimensional Scaling (MDS) across five dimensions: ecological, economic, social, institutional, and infrastructure. The analysis was supported by leverage analysis, Monte Carlo validation, and Geographic Information System (GIS)-based overlay of actual marine space use and official zoning plans. The results showed that ecotourism development in the Gili Matra MPA was moderately sustainable but uneven across dimensions. Institutional sustainability recorded the highest value (63.83), followed by infrastructure (58.32) and economy (56.53), whereas ecological (44.91) and social (45.26) dimensions were less sustainable. Stress values ranged from 10.21% to 17.21%, while R² values ranged from 97.04% to 98.96%, indicating acceptable model performance. Leverage analysis identified the main priority attributes as coastal degradation, waste and pollution pressure, waste and emission treatment infrastructure, harmful products, stakeholder coordination, and social conflict related to tourism and marine resource use. Spatial conformity analysis revealed continued tourism and fisheries activities in zones intended for stronger protection. Sustainable ecotourism development in small-island MPAs requires an integrated and adaptive social–ecological governance approach. Strengthening ecosystem protection, enhancing community participation, improving compliance with zoning regulations, and promoting green infrastructure development are essential prerequisites for long-term sustainability. Further research and integrated interventions should focus on ecological protection and on enhancing community-based monitoring to resolve spatial-use conflicts. ]]>
