The cation exchange capacity (CEC) of soils depends on the amount and composition not only of clay minerals but also of soil organic matter (SOM). While the CEC of soil clay minerals has been intensively studied, little is known about the CEC of organic matter (OM) fractions, in particular those obtained with newly developed SOM extraction techniques. The objective of this study was to develop and test a method to quantitatively determine the CEC of extracted OM fractions and to relate CEC(OM) to OM functional groups possibly responsible for sorption of cations. Water‐ and pyrophosphate‐soluble OM fractions were sequentially extracted from differently managed arable soils of two well‐known long‐term field experiments. The CEC of a freeze‐dried pyrophosphate‐soluble OM fraction [OM(PY)] (0.03 g) mixed with quartz sand (4.97 g) was determined by applying the standard percolation method. The chemical composition of OM(PY) was analyzed by Fourier‐transform infrared (FTIR) spectroscopy. For all plots except those fertilized with farmyard manure, the sorption properties of the OM(PY) fraction were found to be site specific and to reflect soil and crop rotation effects. The relative contribution of the CEC of OM(PY) to the CEC of the soil (0.8–11.6%) is dependent on soil C content and extractability. For all plots, however, the relative contents of carboxylic functional groups in OM(PY) determined with FTIR spectroscopy was found to be linearly related to the CEC of the OM(PY), similar to pure organic substances. This relationship indicates the usefulness of CEC determination on OM(PY) fractions. The results suggest that the relative contents of carboxylic functional groups in OM(PY) reflect long‐term effects of fertilization and crop rotation on the sorption properties of the SOM.