This study aims to investigate the changes in atmospheric deposition trends in Macedonia, using a moss biomonitoring technique. This technique has been used to assess the content of potentially toxic elements in Macedonia in 2002, 2005, 2010, and 2015, within the framework of the International Cooperative Program on Effects of Air Pollution on Natural Vegetation and Crops. The content of 42 elements was analyzed using instrumental neutron activation analysis (INAA), inductively coupled plasma–atomic emission spectrometry (ICP–AES), and atomic absorption spectrometry (AAS), on 72 moss samples collected in the summer of 2015. The median values of the elements studied were compared with data from previous years and with median values obtained from comparable studies in Norway and the neighboring countries. Through factor and cluster analysis, three geogenic factors were identified: Factor 1, which includes the elements Al, Ce, Fe, Hf, La, Li, Na, Sc, Sm, Tb, Ti, Th, V, and U; Factor 4, which includes As, Cl, and I; and Factor 5, which includes the elements Ba and Sr. In addition, one geogenic-anthropogenic factor containing Co, Cr, and Ni (Factor 2), was identified, and one anthropogenic factor containing Cd, Pb, Sb, and Zn (Factor 3). The lead and zinc mines near the towns of Kriva Palanka, Probištip, and Makedonska Kamenica in the eastern region of the country, the former lead and zinc smelter in the town of Veles, and the ferronickel smelter near Kavadarci, have continuously had the greatest anthropogenic impact on the atmospheric deposition of potentially toxic elements during the time period of the study. In addition to the human influences, the lithology and the composition of the soil continue to play a significant role in the distribution of the elements.