Mature landfill leachates are characterized by high levels of ammoniacal nitrogen which must be reduced for discharge in the sewer system and further treatment in municipal wastewater treatment plants. The use of anammox-based processes can allow for an efficient treatment of ammonium-rich leachates. In this work, two real scale sequencing batch reactors (SBRs), designed to initially perform partial nitritation/anammox (PN/A) and simultaneous partial nitrification and denitrification (SPND) for the treatment of ammonium-rich urban landfill leachate, were modelled using BioWin 6.0 in order to enable plant-wide modelling and optimizing. The constructed models were calibrated and validated using data from long- and short-term (one cycle) SBR operation and fit well to the main physical-chemical parameters (i.e., ammonium, nitrite and nitrate concentrations) measured during short-term (one cycle) operations. Despite the different strategies in terms of dissolved oxygen (DO) concentrations and aeration and mixing patterns applied for SBR operation, the models allowed for understanding that in both reactors the PN/A process was shown as the main contributor to nitrogen removal when the availability of organic carbon was low. Indeed, in both SBRs, the activity of nitrite oxidizing bacteria was inhibited due to high levels of free ammonia, whereas anammox bacteria were active due to the simultaneous presence of ammonium and nitrite and their ability to recover from DO inhibition. Increasing the external carbon addition, a prompt decrease of the anammox biomass was observed, with SPND becoming the main nitrogen removal mechanism. Models were also applied to estimate the production rates of nitrous oxide by aerobic ammonia oxidizing bacteria and heterotrophic denitrifiers. The models were found to be a robust tool for understanding the effects of different operating conditions (i.e, temperature, cycle phases, DO concentration, external carbon addition) on the nitrogen removal performances of the two reactors, assessing the contribution of the different bacterial groups involved.