Nitrification and sulfur-based autotrophic denitrification processes can be used to remove ammonia from wastewater in an economical way. However, under certain operational conditions, these processes accumulate intermediate compounds, such as elemental sulphur, nitrite, and nitrous oxide, that are noxious for the environment. In order to predict the generation of these compounds, an analysis based on the Gibbs free energy of the possible reactions and on the oxidative capacity of the bulk liquid was done on case study systems. Results indicate that the Gibbs free energy is not a useful parameter to predict the generation of intermediate products in nitrification and autotrophic denitrification processes. Nevertheless, we show that the specific productions of nitrous oxide during nitrification, and of elemental sulphur and nitrite during autotrophic denitrification, are well related to the oxidative capacity of the bulk liquid.