Microorganisms (Acidithiobacillus ferrooxidanns) are effective in oxidizing ferrous ions that can be used to oxidize pyrite and produce sulfuric acid. Many coal waste resources contain significant concentrations of rare earth elements (REE) and critical materials (CM) that can be extracted using sulfuric acid. These coal waste resources often contain significant concentrations of pyrite, which if not utilized or removed present a future environmental liability for potential acid mine drainage. Thus, the combination of pyrite and REE/CM in coal waste provides a significant resource opportunity for sulfuric acid generation that can be utilized using biooxidation. In addition, the pyrite concentrate used for acid generation also contains REE/CM content that is released during biooxidation of the pyrite concentrate that augments the REE/CM release from the main ore being leached with the acid generated from the pyrite. Thus, this approach provides a very significant environmental advantage as well as augmented REE/CM recovery. Although there are many studies associated with biooxidation in relation to mineral oxidation, there is a lack of information regarding the effects of operating parameters on biooxidation performance and optimization for practical applications. In this study, findings from research in assessing and improving biooxidation for acid generation for REE/CM extraction are presented. Results show that bacteria can very effectively and efficiently oxidize ferrous ions to ferric ions, which oxidize pyrite to produce acid for REE/CM extraction. The factors that showed significant impact on biooxidation performance include air flow rate, stirring speed, residence time, solids concentration, and temperature. The dominance of Leptospirillum ferriphilum species was noted in the bioreactor after a prolonged period of operation, although Acidithiobacillus ferrooxidanns was used in the beginning.