An evaluation of fraction composition and transformation of metal compounds emitted by metal ore processing enterprises and accumulated in soils is crucial for assessing the environmental risks of pollution and ecosystem benefit of remediation. The aim of this study was to develop a suitable sequential fractional procedure for metal pollutants for the peat soils matrix in the impact zone of a Cu-Ni smelter. Three experiment series were performed: (a) the study of the effect of ammonium acetate buffer pH in the range of 3.7–7.8 on the soil metal extraction; (b) the study of the effect of additional volume and frequency of soil treatment with solutions on the content of water-soluble, ammonium acetate extractable, and 0.1 N HNO₃ extractable fractions; and, (c) the determination of the metal fraction composition in the modified technique. Soil treatment with ammonium acetate buffer with a pH range of 4.5–5.5 was the most appropriate for the determination of mobile compounds of Cu and other metals in highly polluted peat soil. Triple soil treatment with water and ammonium acetate is necessary for the complete extraction of the water-soluble and exchangeable fractions, respectively. Additionally, we propose a procedure of full extraction of the exchangeable metal fraction from peat soils while using single treatment with 0.1 N HNO₃. This scheme allows evaluating geochemical mobility of metals and current environmental harm of polluted soils with a high content of organic matter.