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Implementation of onsite bioremediation technologies is essential for textile industries due to rising concerns in terms of water resources and quality. Partial nitritation-anaerobic ammonium oxidation (PN/A) processes emerged as a valid, but unexplored, solution. In this study, the performance of a PN/A pilot-scale (9 m3) sequencing batch reactor treating digital textile printing wastewater (10–40 m3 d−1) was monitored by computing nitrogen (N) removal rate and efficiencies. Moreover, the structure of the bacterial community was assessed by next generation sequencing and quantitative polymerase chain reaction (qPCR) analyses of several genes, which are involved in the N cycle. Although anaerobic ammonium oxidation activity was inhibited and denitrification occurred, N removal rate increased from 16 to 61 mg N g VSS−1 d−1 reaching satisfactory removal efficiency (up to 70%). Ammonium (18–70 mg L−1) and nitrite (16–82 mg L−1) were detected in the effluent demonstrating an unbalance between the aerobic and anaerobic ammonia oxidation activity, while constant organic N was attributed to recalcitrant azo dyes. Ratio between nitrification and anammox genes remained stable reflecting a constant ammonia oxidation activity. A prevalence of ammonium oxidizing bacteria and denitrifiers suggested the presence of alternative pathways. PN/A resulted a promising cost-effective alternative for textile wastewater N treatment as shown by the technical-economic assessment. However, operational conditions and design need further tailoring to promote the activity of the anammox bacteria.