Both natural and anthropogenic factors can cause long-term and irreversible damage to the environment, in particular to the soil. To solve several environmental problems, it is important to study the seasonal changes in the concentration of macro- and trace elements in soil samples and to identify the factors that regulate the concentration of chemical elements in soil and their toxicity This study employs an innovative integrated methodology to detect alterations in the concentrations of certain chemical elements in soil samples from various regions of Armenia throughout the current agricultural seasons. Elemental analysis of soil samples is carried out using a portable XRF analyzer with direct X-ray exposure. The clastogenicity of the soil-plant system was evaluated using Tradescantia (clone 02). A pollution index based on the established Clark concentration for chemical elements was calculated. Trace elements exhibited a higher pollution index than those in other groups. The genotoxic analysis of soils from the study sites revealed a significant increase in soil clastogenicity, beginning in autumn and peaking in the spring season. During the subsequent summer sampling season, all genotoxicity evaluation criteria for the materials under study notably decreased. The results analysis revealed positive and negative correlations among all chemical elements in the soil samples from all sites during the experimental cycle, with varying degrees of significance.