An intensive agricultural management of grassland and agricultural crop land has verifiable effects on chemical, physical and biological properties of the soil. Thereby the loss of organic carbon compounds is a big challenge. Carbon is the most frequent element of soil organic matter, which is necessary for healthy and fertile soils. The application of organic fertilizers is an approved method to increase the carbon pool in soils. The monitoring of such application shall be accomplished by an agricultural trail in Lower Austria (MUBIL), which is cultivated according to the criteria of organic farming. For this purpose the fertilizers alfalfa mulch, biowaste compost and manure were applied over five years on experimental test plots. The effects on the carbon content were investigated on the basis of this experiment besides other parameters. Therefore the parameters organic substance (OS), organic carbon (Corg) and humus content were determined. Fourier Transform Infrared (FTIR) spectroscopy in the near and middle infrared range was used to analyze the stable carbon compounds. Infrared spectra were evaluated by multivariate data analysis such as Principal Component Analysis (PCA) and Partial Least Squares Regression (PLSR) to develop prediction models. After five years an increase of organic substance, organic carbon and humus can be verified for all fertilizer variants. The most important increase was determined for the variants “compost” and “manure”. Changes regarding the stable humic acids could not be approved. Only with increasing depth different humic acid contents could be identified. Based on infrared spectra prediction models for the parameters organic substance, total nitrogen and plant available potassium were developed.