Urban soils are the most vulnerable component of the current terrestrial ecosystem. Due to the anthropogenic influence, various pollutants can accumulate in the soils and have a negative effect on the health of citizens. As a result of the degradation of permafrost landscapes, the disappearance of a number of natural ecosystems, as well as urban areas, is possible. In the course of the development of thermokarst processes, problems arise in the urban environment with the destruction of urban buildings and a decrease in agricultural areas. The ecosystem of Yakutsk city is located in the valley of the Lena River and represents the largest urbanized terrestrial biotope, located in the permafrost-affected bioclimatic and geogenic conditions. This work represents relevant datasets on the physico-chemical, toxicological and agrochemical state of soil cover components in various functional zones of the city. An 3excess of the maximum threshold levels for Zn was noted in the area of active mining within the city borders. From the data obtained of pollution state, the most polluted zone of Yakutsk city is the quarry complex located in relative proximity to the city. In other studied areas of the city, there is no excess of permissible threshold levels for trace elements. According to agrochemical analysis, in Yakutsk city, there is a relatively low content of available agrochemical elements in comparison with other cities located in the permafrost-affected zone.