Background and Aim: The cattle breeding system is facing severe problems associated with the increased negative impact of various human activity areas on the environment and the bodies of farm animals. The use of heavy metals in different production areas leads to their accumulation in the environment due to the ingestion of animals and humans through animal products. This study aimed to assess the elemental composition of the hair and milk of black-spotted cows and to identify the relationship between the content of toxic and essential elements and the state of the intestinal microbiome. Materials and Methods: The element status was estimated by studying the chemical composition of the biosubstrates using inductively coupled plasma-mass spectroscopy. Based on the analysis of hair, the elemental composition, and the use of the coefficient of toxic load, two groups of animals were formed: Group I, which included cows with a lower load factor, and Group II, which included cows with a higher load factor. Results: An increase in the heavy metal concentrations in the hair and milk of animals in Group II was observed. The As, Fe, Pb, Al, Co, Ni, and V concentrations in the hair of cows from Group II increased relative to Group I by 19%, 29%, 24.5%, 32.3%, 35.6%, 21.5%, and 18.2%, respectively. There was a significant increase in the level of Fe by 11.5%, Cr by 8.25%, Mn by 17.6%, Pb by 46.1%, and Cd by 25% in Group II compared with Group I in the assessment of elemental milk composition. There were no apparent changes in the intestinal microbiome of Group II. Conclusion: Some heavy metals were accumulated in the bodies and milk of animals. This shows a high probability of heavy metals causing harm to the health of animals and humans.