Droughts affect terrestrial ecosystems directly and concurrently and can additionally induce lagged effects in subsequent seasons and years. Such legacy effects of drought on vegetation growth and state have been widely studied in tree ring records and satellite-based vegetation greenness, while legacies on ecosystem carbon fluxes are still poorly quantified and understood. Here, we focus on two ecosystem monitoring sites in central Germany with a similar climate but characterised by different species and age structures. Using eddy covariance measurements, we detect legacies on gross primary productivity (GPP) by calculating the difference between random forest model estimates of potential GPP and observed GPP. Our results showed that, at both sites, droughts caused significant legacy effects on GPP at seasonal and annual timescales, which were partly explained by reduced leaf development. The GPP reduction due to drought legacy effects is of comparable magnitude to the concurrent drought effects but differed between two neighbouring forests with divergent species and age structures. The methodology proposed here allows the quantification of the temporal dynamics of legacy effects at the sub-seasonal scale and the separation of legacy effects from model uncertainties. The application of the methodology at a larger range of sites will help us to quantify whether the identified lag effects are general and on which factors they may depend.