Chemolithotrophic organisms conserve energy from oxidation of inorganic compounds. In hydrogen oxidation, organisms couple the oxidation of H2 with the reduction of O2 to form water. ATP is produced in this process when H2 is oxidized by O2 and electron transport reactions generate a proton motive force. An important catalyase in these reactions include the hydrogenase. Some hydrogen bacteria uses a cytoplasmic and a membrane-integrated hydrogenase.

In oxidation of sulfur compounds, sulfur bacteria utilize H2S, S0, S2O3, and SO3 as electron donors. The most common oxidation product is SO4. Some bacteria such as Beggiatoa stores sulfur to create a potential for additional electron processes. One important product of the oxidation of reduced sulfur compounds is protons. Due to proton production, the environment often becomes acidic.

In iron oxidation, ferrous iron is oxidized to ferric iron. At low pHs, very small amounts of energy is available from this reaction so organisms often couple the oxidation of large amounts of iron. Ferric iron produced from ferrous iron is converted to iron precipitates and often lowers pH in aquatic environments. This is also coincident with the acidophilic nature of these organisms.

In nitrification, reduced NH3 and NO2 are oxidized aerobically while ammonia is oxidized anaerobically in anammox. The complete oxidation of NH3 to NO3 involves both the ammonia oxidizers and nitrite oxidizers. Energy from nitrification can be explained by electrons gained from reduction of inorganic materials that enter an electron transport chain to create a proton motive force that in turn, synthesizes ATP. Anammox is carried out by aerobic Bacteria and Archaea that thrive in ammonia rich habitats such as sewers and wastewater. Anammox is considered to be useful in the treatment of sewage.