The main limiting factor, in order to use compost in agriculture, is the total concentration of heavy metals. Natural zeolites, such as clinoptilolite, have the ability to take up and remove those metals by utilizing ion exchange. However, it is important to know about the fractionation of the heavy metals during the thermophilic phase and the maturation phase. The purpose of this work was to determine the changes in the fraction of heavy metals in sewage sludge compost in which clinoptilolite is used as a bulking agent to remove metals. The final result indicates that a significant (p < 0.05) percentage of the metals, which is not removed by the zeolite, is associated with the residual fraction which is considered as an inert form.