This study deals with the influence of heterotrophic growth on autotrophic nitrogen removal from wastewater in a granular sludge reactor. A mathematical model was set-up including autotrophic and heterotrophic growth and decay in the granules from a partial nitritation-anammox process. A distinction between heterotrophic bacteria was made based on the electron acceptor (dissolved oxygen, nitrite or nitrate) on which they grow, while the nitrogen gas produced was ‘labelled’ to retrieve its origin, from anammox or heterotrophic bacteria. Taking into account heterotrophic growth resulted in a lower initial nitrogen removal, but in a higher steady state nitrogen removal compared with a model in which heterotrophic growth was neglected. The anammox activity is related with the fact that heterotrophs initially use nitrite as electron acceptor, but when they switch to nitrate the produced nitrite can be used by anammox bacteria. Increased anammox activity in the presence of heterotrophs, therefore, resulted in a marginally increased N2 production at steady state. Heterotrophic denitrification of nitrate to nitrite also explains why small amounts of organic substrate present in the influent positively affect the maximum nitrogen removal capacity. However, the process efficiency deteriorates once the amount of organic substrate in the influent exceeds a certain threshold. The bulk oxygen concentration and the granule size have a dual effect on the autotrophic nitrogen removal efficiency. Besides, the maximum nitrogen removal efficiency decreases and the corresponding optimal bulk oxygen concentration increases with increasing granule size.