The complexity of ecosystem processes, especially under continuously changing environmental conditions, requires high resolution insight into ecosystem carbon fluxes. It is essential to gain not only information about relative carbon balance and fluxes (common for partitioning studies), but also in absolute mass units. To evaluate absolute fluxes in belowground carbon pools, eddy covariance and stable isotope labeling were coupled in a 21 day experiment in summer 2010. Eddy covariance based net ecosystem exchange was measured on extensively managed grassland and separated into underlying assimilation and ecosystem respiration by a carbon flux partitioning model. Resultant CO₂ assimilation served as absolute carbon input into the ecosystem that was further partitioned by applying the relative carbon distribution in subsidiary pools, gained by 13C pulse labeling and tracing. In doing so, the mean daily assimilation of –7.1 g C m^–2 d^–1 was partitioned into fluxes of 2.5, 0.8, 0.5, 2.3 and 1.0 g C m^–2 d^–1 into shoots, roots, soil, shoot respiration and CO₂ efflux from soil, respectively. Finally, it was concluded that the approach is suitable as an upgrade for both, atmospheric flux measurements and isotopic partitioning methods.