The main bottleneck to maintain the long-term stability of the partial nitritation-anammox processes, especially those operated at low temperatures and nitrogen concentrations, is the undesirable development of nitrite oxidizing bacteria (NOB). When this occurs, the punctual addition of compounds with the capacity to specifically inhibit NOB without affecting the process efficiency might be of interest. Sodium azide (NaN3) is an already known NOB inhibitor which at low concentrations does not significantly affect the ammonia oxidizing bacteria (AOB) activity. However, studies about its influence on anammox bacteria are unavailable. For this reason, the objective of the present study was to evaluate the effect of NaN3 on the anammox activity. Three different types of anammox biomass were used: granular biomass comprising AOB and anammox bacteria (G1), anammox enriched granules (G2) and previous anammox granules disaggregated (F1). No inhibitory effect of NaN3 was measured on G1 sludge. However, the anammox activity decreased in the case of G2 and F1. Granular biomass activity was less affected (IC50 90 mg/L, G2) than flocculent one (IC50 5 mg/L, F1). Summing up, not only does the granular structure protect the anammox bacteria from the NaN3 inhibitory effect, but also the AOB act as a barrier decreasing the inhibition.