Global environmental change is characterized by changing climate, atmospheric composition and land use. Its impact on ecosystem structure and functioning has been detected throughout the world. While every ecosystem is vulnerable to climate change, the degree of the impact and the magnitude of the ecosystem response are likely to vary. Protected areas of South America provide a ‘laboratory’ to test expectations of climate change effects on ecosystems at a regional scale. By using protected areas we minimized the effects of land use/land cover changes over ecosystem functioning. We analyzed the temporal trends, that is, directional changes, and spatial heterogeneity of both climatic variables and attributes of the seasonal dynamics of the normalized difference vegetation index, that is, a surrogate of vegetation carbon gains derived from satellite information, on 201 protected areas of South America. Increased productivity and higher seasonality, frequently climate driven, is the most common signal across South American biomes but concentrated on those areas located in the tropics and subtropics. In general, arid and semiarid sites responded positively to increases in precipitation and negatively to increases in temperature, while humid ecosystems responded in the opposite way. Our results provide a preliminary basis for predicting which ecosystems will respond more rapidly and strongly to climate change. We also provide support to the fact that protected areas are not static systems as their functioning is changing with different magnitude and in contrasting directions.