Soil organic carbon loss occurs at a rate equivalent to 10 % of the total fossil fuel emissions for Europe as a whole. Intensive use of synthetic fertilizers results in soil degradation and nutrient loss. Microbially mediated soil organic matter is an extremely sensitive pool that indicates subtle changes in the quality parameters responsible for the soil’s ecological and productive functions. The goal of the research was calculation of carbon budget and changes in carbon accumulation/sequestration as a result of more than 50 years of mineral fertilization. Stocks of C in organic carbon, labile carbon, light carbon and microbial carbon fractions were analyzed, as well as carbon sequestration rate in 50-yrs were calculated. The highest input of organic C, PMC LFC and MBC was found for the treatments with the highest N-fertilization. However, C sequestration rates of the fertilized plots were from 10.68 – to 12.12 % from the 100% adjacent natural meadow. C sequestration rate between the fertilized plots were not significantly different except for the control plot for each studied fraction of carbon (OC, PMC, LFC and MBC). The sensitivity index correlated with the amount of light-fraction OM. The results give a deeper insight into the behavior of different pools of labile SOM in the agro-landscapes and can serve as a reliable basis for further researches focused on neutral carbon emissions and effective C sequestration