Bioleaching research considers both the bio- and anthroposphere in the search for novel ways to recover resources and elements, which is important to the concept of sustainable development. Since the efficient, cost-effective and simple recovery of resources is of increasing importance in the circular economy model, the bioleaching of metals is a method currently gaining interest. The process is also of importance considering the need for the neutralization of waste materials/resources that allow for their safe storage and use. In this study, Acidithiobacillus thiooxidans bacteria, which is commonly found and widely utilized in the bioleaching process due to its high tolerance to heavy metals, was used in a twenty-eight-day experiment. The manner in which bacteria inhabit incineration residues was observed using fluorescence optical microscopy and scanning electron microscopy. The concentration of elements in incineration residues and in the post-reaction solutions was measured using inductively coupled plasma mass spectrometry and the efficiency of element recovery was calculated based on the results. Municipal waste incineration bottom ash and sewage sludge incineration fly ash were considered in the experiment. The extraction rates were far from satisfactory, with the average 20 and 50% for bottom ash and sewage sludge ash, respectively. The obtained results were consistent with microscopic observations where the relative number of bacteria increased only slightly over time in the sewage-sludge fly ash and was barely observed in the bottom ash of municipal- -waste incineration.