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In agricultural soils, the formation of soil organic matter largely depends on the carbon (C) input by crop residues and rhizodeposition, which is thus of decisive importance for the management and prediction of soil organic carbon (SOC) stocks in cropland and grassland. However, there is a remarkable lack of reliable, crop-specific C input data. We used a plant C allocation approach to estimate the C input of major crops and grassland into agricultural soils of Bavaria in southeast Germany. Historic and recent plant C allocation coefficients were estimated and C inputs were calculated for a 60-year period (1951–2010) using long-term agricultural statistics. The spatial distribution of C inputs within Bavaria was derived from county-specific statistical data. The results revealed increases of the C input by 107–139% for cereals, 173–188% for root, forage and leguminous crops and 34% for grassland in the last 60 years. This increase was related to linear yield increases until 1995 despite significant changes of plant C allocation. However, from 1995 onwards, crop yields and related C inputs stagnated, which allowed a robust estimation of recent crop-specific C input values. A total C input of 3.8–6.7 t ha −1 yr −1 was estimated for cereals, 5.2–6.3 t ha −1 yr −1 for root, forage and leguminous crops and 2.4 t ha −1 yr −1 for grassland. These amounts were partly higher compared to estimations in the literature. A generally high spatial variability of C inputs was detected within Bavaria with differences of up to 40% between adjacent counties. The results of this study could be used to optimize the C input of crop rotations and thus promote the formation of soil organic matter and C sequestration in agricultural soils on the basis of a soil carbon model. Moreover, recent estimations of C inputs could be used to model the future development of agricultural SOC stocks. A further stagnation of crop yields and the related C input under an ongoing temperature increase bears the risk of a future decrease of SOC stocks in cropland soils of Bavaria. [ABSTRACT FROM AUTHOR]