Assessing ecosystem functioning is crucial for managing and conserving ecosystems and their services. Numerous ways to evaluate ecosystem functioning have been developed, using species traits, such as Plant Functional Types (PFTs), flux measurements with Eddy Covariance (EC) technique, and remote sensing techniques. We propose that the spatial heterogeneity in ecosystem functioning at a regional scale can be assessed and monitored using satellite-derived Ecosystem Functional Types (EFTs): groups of ecosystems or patches of the land surface that share similar dynamics of matter and energy exchanges. We hypothesize that, as observed for PFTs, different EFTs should have distinct patterns and magnitudes of Net Ecosystem Exchange (NEE) of carbon dioxide measured using the EC technique. We derived EFTs based on the 2001–2014 time-series of satellite images of the Enhanced Vegetation Index (EVI) and compared them with NEE measurements (derived from in situ field observations using the EC technique) across 50 European sites. Our results show that distinct EFTs classes display significantly different dynamics and magnitudes of NEE and that EFTs perform marginally better than PFTs in explaining NEE regional patterns. Land-cover maps based on PFTs are difficult to update on an annual basis and are not sensitive to changes in ecosystem performance (e.g., droughts or pests) that do involve short-term changes in PFT composition. In contrast, satellite-derived EFTs are sensitive to short-term changes in ecosystem performance. Satellite-derived EFTs are an ecosystem functional classification built from satellite observations that allow the identification of homogeneous land patches in terms of ecosystem functions, e.g., ecosystem net productivity measured on the ground as NEE. Satellite-derived EFTs can be recalculated annually, providing a straightforward way to assess and monitor interannual changes in ecosystem functioning and functional diversity.