Studies of the carbon sink of forest ecosystems often stratify the studied stands by the dominating species and thereby abstract from differences in the mixed-species, multi-cohort structure of many forests. This case study infers whether the aggregation of forestry data introduces a bias in the estimates of carbon stocks and their changes at the scale of individual stands and the scale of a forest district. The empirical TreeGrOSS-C model was applied to 1616 plots of a forest district in Central Germany to simulate carbon dynamics in biomass, woody debris, and soil. In a first approach each stand was explicitly simulated with all cohorts. In three other approaches the forest inventory data were aggregated in several ways, including a stratification of the stands to 110 classes according to the dominating species, age class, and site conditions. A small but significant bias was confirmed. At stand scale the initial ecosystem carbon stocks by the aggregated approach differed from that of the detailed approach by 2.3%, but at the district scale only by 0.05%. The differences in age between interspersed and dominant cohorts as well as differences in litter production were important for the differences in initial carbon stocks. The amounts of wood extracted by thinning operations were important for the differences in the projection of the carbon stocks over 100 years. Because of the smallness of bias, this case study collects evidence that the approaches, that represent stands or stratums by a single cohort, are valid at the scale of a forest district or larger.