In stationary field experiments in the forest-steppe of Western Siberia, it was shown that long-term agricultural use of soil without the use of fertilizers caused a decrease in the soil content of heavy metals related to plant micronutrients — Cu, Zn, Co; the level of Pb, Cr, Sr has changed slightly. It was established that the long-term application of high, agronomically justified doses of mineral fertilizers, accompanied by a significant increase in the yield of cultivated crops, did not lead to an increase in the content of HM in the soil, compared with not fertilized areas. It was revealed that the unbalanced use of fertilizers, not ensured by the growth of crop productivity, contributed to the accumulation of HM in the soil. The necessity of monitoring the agro-ecological state of soils of agrocenoses in order to identify both excessive accumulation of heavy metals and micronutrient deficiency is substantiated.