Pyrophoric iron sulfides formed as a result of oil cracking, when in contact with air oxygen, have the ability to self-ignite, as a result of which they are highly explosive at oil refining enterprises. It is known that oil refineries in Kazakhstan produce from 4 to 10 tons per year of this hazardous waste. The main idea of the study was to use the biochemical abilities of microorganisms, in particular the thionic bacteria Acidithiobacillus ferrooxidans, to change the physico-chemical properties of pyrophoric iron sulfides. In this regard, the aim of the study was to study the possibility of using A. ferrooxidans for deactivation of pyrophoric iron sulfides at an oil refinery in the south of Kazakhstan. It was found that the cultivation of a strain of thionic bacteria A. ferrooxidans ThIO1 in solutions with pyrophoric iron sulfides as the only source of divalent iron and compliance with optimal conditions for their vital activity: +280C, pH 2.0-2.5, S:L=1:10±2 will decontaminate explosive waste of oil and gas industry enterprises. The method of biological decontamination of pyrophoric iron sulfides was introduced at the PetroKazakhstan Oil Products LLP refinery on the Southern Kazakhstan in 2007. For the successful implementation of this method at other enterprises, it is necessary to develop a special adapted industrial installation for the biological decontamination of pyrophoric deposits with continuous (in the case of receiving waste from different enterprises of Kazakhstan) or periodic cultivation of microorganisms, compliance with optimal parameters for the vital activity of microorganisms.