Ballasted tracks are the commonly used railway track systems with constant demands for reducing maintenance cost and improved performance. Elastic layers are increasingly used for improving ballasted tracks. In order to better understand the effects of elastic layers, physical understanding at the ballast particle level is crucial. Here, discrete element method (DEM) is used to investigate the effects of elastic layers – under sleeper pad (USP) at the sleeper/ballast interface and under ballast mat (UBM) at the ballast/bottom interface – on micro-mechanical behavior of railway ballast. In the DEM model, the Conical Damage Model (CDM) is used for contact modelling. This model was calibrated in Suhr et al. (Granul Matter 20(4):70, 2018) for the simulation of two different types of ballast. The CDM model accounts for particle edge breakage, which is an important phenomenon especially at the early stage of a tamping cycle, and thus essential, when investigating the impact of elastic layers in the ballast bed. DEM results confirm that during cyclic loading, USP reduces the edge breakage at the sleeper/ballast interface. On the other hand, UBM shows higher particle movement throughout the ballast bed. Both the edge breakage and particle movement in the ballast bed are found to influence the sleeper settlement. Micro-mechanical investigations show that the force chain in deeper regions of the ballast bed is less affected by USP for the two types of ballast. Conversely, dense lateral forces near to the box bottom were seen with UBM. The findings are in good (qualitative) agreement with the experimental observations. Thus, DEM simulations can aid to better understand the micro-macro phenomena for railway ballast. This can help to improve the track components and track design based on simulation models taking into account the physical behavior of ballast.