Extreme weather events pose a growing threat to the stability of terrestrial ecosystems, and understanding how ecosystems respond remains a critical challenge. This study explores how extreme weather conditions affect the persistence of net ecosystem exchange (NEE) of CO₂ in forest ecosystems. Using Detrended Fluctuation Analysis (DFA), we quantify persistence and assess changes in carbon flux stability under stress. By analysing high-frequency carbon flux data across multiple European sites, we reveal that ecosystem persistence is tightly linked to hydrological conditions, particularly soil moisture. Moreover, we show that large drops in persistence can signal periods of ecosystem stress. Our findings show that drought–heat compound events can diminish resilience and prolong recovery times, with temperate and boreal forests lacking heat or drought adaptations emerging as especially vulnerable. Furthermore, these stress pulses alter carbon dynamics long after the event, suggesting physiological damage that heightens sensitivity to future weather fluctuations. Overall, identifying changes in persistence could signal potential ecological destabilisation, providing key insights into how terrestrial ecosystems might cope with intensifying climate extremes.