Heterotrophic pretreatment combined with autotrophic bioleaching of Polkowice black shale were studied. Combination of these two processes was introduced as two-stage process which turned out to be more efficient in the terms of metals extraction. The sequence of preliminary heterotrophic and further autotrophic bioleaching was found as most reliable processing manner, since heterotrophic process provides the material’s surface area expansion, and therefore strong influences rate and efficiency of autotrophic leaching. Besides, it was found that tube bioreactors designed specially for hereby research ensure better processing condition than Erlenmeyer flasks in the terms of extraction speed and efficiency.