Currently, there exists growing evidence that warming is amplified with elevation resulting in rapid changes in temperature, humidity and water in mountainous areas. The latter might result in considerable damage to forest and agricultural land cover, affecting all the ecosystem services and the socio-economic development that these mountain areas provide. The Mediterranean mountains, moreover, which host a high diversity of natural species, are more vulnerable to global change than other European ecosystems. The protected areas of the mountain ranges of peninsular Spain could help preserve natural resources and landscapes, as well as promote scientific research and the sustainable development of local populations. The temporal statistical trends (2001–2016) of the MODIS13Q1 Normalized Difference Vegetation Index (NDVI) interannual dynamics are analyzed to explore whether the NDVI trends are found uniformly within the mountain ranges of mainland Spain (altitude > 1000 m), as well as in the protected or non-protected mountain areas. Second, to determine if there exists a statistical association between finding an NDVI trend and the specific mountain ranges, protected or unprotected areas are studied. Third, a possible association between cover types in pure pixels using CORINE (Co-ordination of Information on the Environment) land cover cartography is studied and land cover changes between 2000 and 2006 and between 2006 and 2012 are calculated for each mountainous area. Higher areas are observed to have more positive NDVI trends than negative in mountain areas located in mainland Spain during the 2001–2016 period. The growing of vegetation, therefore, was greater than its decrease in the study area. Moreover, differences in the size of the area between growth and depletion of vegetation patterns along the different mountains are found. Notably, more negatives than expected are found, and fewer positives are found than anticipated in the mountains, such as the Cordillera Cantábrica (C.Cant.) or Montes de Murcia y Alicante (M.M.A). Quite the reverse happened in Pirineos (Pir.) and Montes de Cádiz y Málaga (M.C.M.), among others. The statistical association between the trends found and the land cover types is also observed. The differences observed can be explained since the mountain ranges in this study are defined by climate, land cover, human usage and, to a small degree, by land cover changes, but further detailed research is needed to get in-depth detailed conclusions. Conversely, it is found that, in protected mountain areas, a lower NDVI pixels trend than expected (>20%) occurs, whereas it is less than anticipated in unprotected mountain areas. This could be caused by management and the land cover type.