<p>The sustainable production of high-value crops such as saffron requires integrated management frameworks. The water–energy–food (WEF) nexus provides a comprehensive approach for optimizing resource use and addressing trade-offs among interconnected agricultural systems. However, empirical evidence on the application of the WEF nexus in organic saffron production remains limited. This study assesses the sustainability status of water, energy, and food dimensions using a robust set of indicators evaluated by an expert panel with extensive experience in saffron cultivation. Sustainability indicators were standardized on a scale ranging from 0 (lowest sustainability) to 1 (highest sustainability). The overall sustainability index for food (0.373) was substantially lower than that of water (0.880) and energy (0.648), indicating that the food dimension represents the most vulnerable component of organic saffron production systems. Sub-dimension analysis further revealed heterogeneous performance across sustainability components. Economic and market-related indicators (0.219) demonstrated relatively stronger performance, whereas social participation and indigenous knowledge (0.049), technological and infrastructural support (0.019), and ecological and environmental management (0.086) exhibited weak sustainability outcomes. Overall, economic factors currently contribute most significantly to sustainability across all WEF components, while technological, infrastructural, social, and ecological dimensions remain comparatively underdeveloped. These findings highlight the need for targeted interventions in technology adoption, infrastructure development, social engagement, and ecological management to enhance the resilience and sustainability of organic saffron production systems. The results provide actionable insights for policymakers and farm managers to guide investment priorities, capacity building, and the development of organic production standards aimed at strengthening sustainable high-value agriculture.</p>