One of the problems associated with polymetallic ore concentration is the separation of bulk concentrates, which is difficult due to the textural and structural characteristics of mineral particles. In this paper, we proposed selective bioleaching of zinc and nickel from bulk copper-zinc and copper-nickel sulfide concentrates, respectively, to extract these metals into solution and to produce high-grade copper concentrates. In the copper-zinc concentrate, zinc occurred in sphalerite (ZnS). In the copper-nickel concentrate, nickel occurred in pentlandite ((Ni,Fe)9S8) and violarite (FeNi2S4). In both concentrates, which also contained pyrite (FeS2) and pyrrhotite (Fe1-xS), copper occurred in chalcopyrite (CuFeS2). Bioleaching of the concentrates by acidophilic microbial communities at 30 and 40 °C was compared. Bioleaching at increased temperature was characterized by the higher intensity of the process. Complete removal of zinc from the copper-zinc concentrate occurred within 15 days at 30 °C and 4 days at 40 °C, while the copper content in the bioleach residue increased by 7.5 and 5.9%, respectively. Nickel leaching was less efficient: 67.6% at 30 °C and 86.7% at 40 °C after 22 days of the process. At the same time, the copper content in the bioleach residue increased by 2.7 and 5.7%. Dissolution of violarite proceeded more rapidly than that of pentlandite. More efficient zinc and nickel leaching from the concentrates at 40 °C could be associated with a higher microbial diversity in the communities formed at this temperature. An increase in the proportion of bacteria of the genera Sulfobacillus and Ferrimicrobium, as well as archaea of the families Ferroplasmaceae and Cuniculiplasmataceae, was shown. At both temperatures, Acidithiobacillus and Leptospirillum bacteria prevailed during the biooxidation of both, the copper-zinc and copper-nickel concentrates.