The terrestrial carbon fluxes show the largest variability among the components of the global carbon cycle and drive most of the temporal variations in the growth rate of atmospheric CO 2. Understanding the environmental controls and trends of the terrestrial carbon budget is therefore essential to predict the future trajectories of the CO 2 airborne fraction and atmospheric concentrations. In the present work, patterns and controls of the inter-annual variability (IAV) of carbon net ecosystem exchange (NEE) have been analysed using three different data streams: ecosystem-level observations from the FLUXNET database (La Thuile and 2015 releases), the MPI-MTE (model tree ensemble) bottom–up product resulting from the global upscaling of site-level fluxes, and the Jena CarboScope Inversion, a top–down estimate of surface fluxes obtained from observed CO 2 concentrations and an atmospheric transport model. Consistencies and discrepancies in the temporal and spatial patterns and in the climatic and physiological controls of IAV were investigated between the three data sources. Results show that the global average of IAV at FLUXNET sites, quantified as the standard deviation of annual NEE, peaks in arid ecosystems and amounts to ∼ 120 gC m −2 y −1, almost 6 times more than the values calculated from the two global products (15 and 20 gC m −2 y −1 for MPI-MTE and the Jena Inversion, respectively). Most of the temporal variability observed in the last three decades of the MPI-MTE and Jena Inversion products is due to yearly anomalies, whereas the temporal trends explain only about 15 and 20 % of the variability, respectively. Both at the site level and on a global scale, the IAV of NEE is driven by the gross primary productivity and in particular by the cumulative carbon flux during the months when land acts as a sink. Altogether these results offer a broad view on the magnitude, spatial patterns and environmental drivers of IAV from a variety of data sources that can be instrumental to improve our understanding of the terrestrial carbon budget and to validate the predictions of land surface models.