Abstract Seven years of continuous eddy covariance measurements at an alpine meadow were used to investigate the impacts of climate drivers and ecosystem responses on the inter-annual variability (IAV) of the net ecosystem exchange (NEE). The annual cumulative value of NEE was positive (source) in 2003, 2005 and 2009 (50, 15 and 112 g m−2 respectively) and negative (sink) in 2004, 2006, 2007 and 2008 (29, 75, 110 and 28 g m−2 respectively). The IAV of carbon dioxide fluxes builds up in two phenological phases: the onset of the growing season (triggered by snow melting) and the canopy re-growth after mowing. Respiratory fluxes during the non-growing season were observed to increase IAV, while growing season uptake dampened it. A novel approach was applied to factor out the two main sources of IAV: climate drivers’ variability and changes in the ecosystem responses to climate. Annual values of carbon dioxide fluxes were calculated assuming (a) variable climate and variable ecosystem response among years, (b) variable climate and constant ecosystem response and (c) constant climate and variable ecosystem response. The analysis of flux variances calculated under these three assumptions indicates the occurrence of an important negative feedback between climate and ecosystem responses. Due to this feedback, the observed IAV of NEE is lower than one would expect for a given climate variability, because of the counteracting changes in ecosystem responses. This alpine meadow therefore demonstrates the ability to acclimatise and to limit the IAV of carbon fluxes induced by climate variability.