<p>Monitoring biodiversity in protected areas is essential to mitigate biodiversity loss and evaluate the effectiveness of conservation policies. Integrating satellite remote sensing technologies, ecological niche models, and time-series analyses of biodiversity trends offers a fast and robust approach for assessing habitat suitability changes and species vulnerability over time. In this study, we implemented a framework combining these tools to monitor biodiversity in the Montesinho/Nogueira Special Conservation Area (Northeast Portugal). Using the MaxEnt algorithm, we generated ecological niche models for 342 species based on a time series (2001–2023) of remote sensing data from the Moderate-Resolution Imaging Spectroradiometer (MODIS) sensor. We analysed habitat suitability trends with the Mann-Kendall test to detect changes in habitat quality, as a metric of species vulnerability for individual species, five major taxonomic groups (vascular flora, amphibians, reptiles, birds, and mammals), functional groups (e.g. climate affinity, habitat type, diet, activity, reproduction), and conservation status (regional and European levels). Our study revealed a significant decline in habitat suitability over the past two decades, impacting all taxonomic groups and ecological functions. We observed a high variability in habitat suitability trends among species and taxonomic/functional groups, highlighting the complexity of biodiversity responses to environmental changes. Functional traits such as climatic affinity, trophic level or habitat specialisation were associated with variable rates of habitat decline, with species of Atlantic affinity, species associated with croplands and wetlands, and species specialised in insectivorous diets being at higher risk. Overall, these findings emphasise the need for comprehensive biodiversity monitoring programmes and demonstrate the utility of our approach to inform evidence-based conservation strategies in protected areas globally.</p>