Thermophilic nitrogen removal via partial nitritation/anammox (PN/A) could be a major breakthrough for treating nitrogenous warm wastewaters devoid of organic carbon. However, the knowledge on the microbial ecology and process dynamics to integrate PN and A at thermophilic temperatures is lacking. This thesis focusses on developing single stage thermophilic PN/A at 50°C and manage the interactions between the different microbial guilds in three different biofilm configurations: a granular reactor, moving bed biofilm reactor (MBBR), and membrane aerated biofilm reactor (MABR). Studying the ecology of PN/A under these three configurations will enable understanding how the substrate availability and environmental conditions influences the microbial interactions, stratification and the overall nitrogen removal capacity in each biofilm structure. The project will investigate key strategies for long-term suppression of nitrite oxidizing bacteria (NOB) for a stable PN/A integration and will study the stability of the process towards varying conditions, such as pH and temperature, as well as the effect of the presence of influent organic carbon. Kinetic modelling will be used to simulate the community behaviour and stratification in response to process conditions. Finally, the thermophilic PN/A will be applied to the treatment of a real wastewater. The project will unveil the most suitable configuration to carry out long-term PN/A with maximum N removal and minimal GHG emissions.