The importance of management increases in the context of numerous and intensive inner and outer pressures on Protected Areas (PAs). The need to assess the management effectiveness (ME) in protected areas is increasing around the world. The ME assessment helps to improve the management of PAs and to develop a rational, long-term action plan. This study was conducted using the World Wildlife Fund for nature (WWF) Management Effectiveness Tracking Tools methodology (METT) to evaluate the ME of six PAs in central and eastern regions of Mongolia. The main purpose of this study was to assess ME and identify common threats of PAs across different natural zones and administrative areas in Mongolia. The results of this evaluation indicate that, the main threats faced by PAs in Mongolia are: (i) degradation of ecosystems, (ii) environmental pollution, and (iii) habitat fragmentation, resulting from over-exploitation and inappropriate use of natural resources. All six PAs examined have clear management goals and management decision-making systems however, their ME scores differ significantly. This research suggests that the administrative features of the individual PA influence management effectiveness and problems in the efficient implementation of management still need to be resolved.