Phosphorus-containing wastes formed after the production of phosphorus fertilizers in Shymkent, due to intensive urbanization were within the city limits and for reason of processes of water-wind erosion began to pose a serious threat to the environment and the population of the city. It was found that the formation of the fractional composition of wastes was influenced by the conditions of processing of raw materials, weather and climatic parameters and time characteristics of storage. The greater part of the waste are silicate and calcium-containing compounds. One of the options for waste disposal is considered the possibility of bio-leaching of valuable components from it. The choice of phase 1 nitrifies and micromycetes is justified by neutral or slightly acidic pH values of their cultivation, which will allow to abandon the use of acidophilic bacteria or sulfuric acid leaching. A variant using a strain of acidophilic bacteria Alicyclobacillus tolerans ST confirmed the effectiveness of their use in the bioleaching of magnesium, aluminum, potassium, calcium, phosphorus, REE such as lanthanum, cerium and neodymium. The use of micromycete Aspergillus niger AsIA proves its effectiveness in the extraction of zirconium and silver. The use of nitrifying bacteria Methyloversatilis thermotolerans MSO increases the extraction of barium and iron.