Within the expanding wind energy projects context, this study explores the intricate relationship between biodiversity conservation and wind power development in the Cantabrian Mountains. By analyzing data from 1107 UTM grids measuring 10 × 10 km, we have identified 378 endangered vascular plant taxa and 36 bryophytes, including 135 that are regional endemics. Wind power complexes pose a significant risk of irreversible impacts on plant conservation zones and their integrity if proper management informed by the best available scientific knowledge is not implemented. This study introduces the concept of very important plant areas (VIPAs) as a crucial tool for identifying priority conservation areas. A total of 60% of the UTM grids were classified in the “high conservation value” category. Among the endangered species within the region, only 11% are afforded protection at the European level and 17% at the national level, leaving a key role for regional governments with heterogeneous lists. Our findings highlight the urgent need for legislation that accommodates updates to protected species lists, ensuring the inclusion of high-risk taxa and legally binding mechanisms at various administrative tiers. The proposed method relies on quantifiable and repeatable criteria, making it adaptable for application in other territories and for broader land use planning purposes.