This study investigates the feasibility of using batch assays combined with microbial community analysis to control the partial nitritation/anammox (PN/A) process. A Moving Bed Sequencing Batch Biofilm Reactor (MBSBBR) was operated over 130 days with varying ammonia influent concentrations. The highest anammox activity (22.4mgN/gVSS∙h) was observed at an influent concentration of 200 mg N-NH4/L, correlating with high total inorganic nitrogen (TIN) removal efficiency. However, increasing the ammonia influent concentration to 340mgN/L led to decreased anammox and nitrifying bacteria activities and reduced TIN removal efficiency. Sequencing revealed Candidatus Brocadia as the predominant genus, with its abundance correlating with TIN removal performance. High correlation coefficients (above 0.76) among batch tests highlighted the interdependence of key bacterial activities in the PN/A, emphasizing the need for a balanced microbial community for effective nitrogen removal. Batch assays provided immediate data on metabolic activities, while sequencing offered comprehensive insights into microbial community structure. Integrating these methods allowed for a holistic understanding of the microbial dynamics and their impact on process stability. This approach enhances the accuracy of wastewater treatment monitoring, aiding in the development of effective management strategies for optimizing PN/A processes.