Soil organic matter (SOM) can be affected by adopted soil management options. However, it is unclear how mineral and organic fertilization could change the amount and composition of SOM. The objective of this study was to test the applicability of infrared spectroscopy for analyzing management-induced impacts on organic matter (OM) composition. Ap horizon samples were collected from the long term-field experiments at Bad Lauchstädt (loam), Groß Kreutz, and Müncheberg (both loamy sand) in plots fertilized with farmyard manure (FYM), farmyard manure plus mineral N (FYM + N), and mineral N only (N) and an unfertilized control plot. The SOM and hot-water-soluble and pyrophosphate-soluble (OM-PY) organic matter fractions were analyzed using Fourier-transform infrared (FTIR) spectroscopy. The OM composition was evaluated in terms of the ratio between absorption band intensities in FTIR. The soluble OM fractions of FYM had larger C=O/C–O–C ratios than the N and control treatments. While the cation exchange capacity (CEC) of OM-PY from FYM was larger, it was smaller for the N plots than the control at all sites. The results allowed identification of fertilization-induced long-term dynamics in (i) the OM composition and (ii) the CEC and the potential wettability of SOM and OM fractions. The OM-PY fraction could be used to identify and characterize the long-term changes in OM composition. For a more quantitative analysis, however, more replicate samples and a seasonal differentiation would be required to separate between shorter and longer term changes.