Changes and shifts in how land is used and covered (LULC) continue to reshape Ecosystem Services in Mediterranean mountain regions. With approximately 1,398,500 hectares, the Atlas Cedar Biosphere Reserve (ACBR) represents a large, protected area in central Morocco. This study develops a spatial analysis to assess the impacts of LULC dynamics on carbon storage and sequestration across the ACBR between 1995 and 2025, based on the InVEST Carbon Storage and Sequestration Model. LULC changes were quantified using multiple GIS and remote sensing techniques; historical data (1995) were obtained from global land cover datasets, while current maps (2025) were extracted from the Sentinel-2-derived Dynamic World dataset via Google Earth Engine. Seven LULC classes were reclassified (Forests, Croplands, Bare ground, Built-up areas, Shrubs and scrub, Water bodies, and Grasslands). Carbon pools were parameterized using synthesized data from previous Moroccan studies and global inventories. To ensure accurate long-term change detection, we utilized the rigorously validated GLC FCS30D and Dynamic World datasets, yielding reliable classification accuracies between 72% and 81% across the study period (30 years). The results highlight a decrease in carbon storage from 13.404×10⁹ Mg C in 1995 to 11.292×10⁹ Mg C in 2025, a net loss of 2.111×10⁹ Mg C. Vegetation transitions revealed that bare ground dominated absolute area changes, while croplands and grasslands suffered the greatest absolute and relative carbon losses. Findings underscore the importance of forest areas as dominant carbon reservoirs and serve as a critical warning sign that combined pressures of global warming and localized anthropogenic disturbances actively threaten the ecological integrity and carbon sink efficiency of even strictly protected biosphere reserves. This study highlights the urgent need to integrate landscape policies to protect high-carbon ecosystems and strengthen Morocco’s commitments to UNESCO’s MAB and climate change strategies.