BACKGROUND Partial nitrification-anammox (PN-A) is a widely recognized technology to remove nitrogen from different types of wastewater. Low oxygen concentration is the most used strategy for PN-A start-up, but stability problems arise during the operation; thus, in the present study the effects of the type of agitation, oxygenation and shear stress on the sensitivity, energy consumption and performance were evaluated. Recognition of these parameters allows considered choice of the design of an industrial process for nitrogen abatement. RESULTS A mechanically agitated reactor (MAR) was compared to a stable, long-term operation period bubble column reactor (BCR), both started under low dissolved oxygen concentration conditions. MAR microbial assays confirmed the destruction of the nitrifying layer and an imbalance of the entire process when the oxygen to nitrogen loading ratio (O-2:N) decreased by 25%. The granule sedimentation rate and specific anammox activity were 17% and 87% higher (respectively) in BCR. Economic analysis determined that the cost of aeration for the MAR and for the BCR were 23.8% and 1% of the total PN-A energy consumption, respectively. CONCLUSIONS The BCR showed better results than the MAR. This study highlights the importance of type of agitation, oxygenation and shear stress for industrial-scale PN-A designs. (c) 2018 Society of Chemical Industry