Start-up and operation of single-stage nitritation/anammox reactor employing complete autotrophic nitrogen can be difficult. Keeping the performance criteria and monitoring the microbial community composition may not be easy or fast enough to take action on time. In this study, a control strategy is developed based on stoichiometric analysis of monitored nitrogen species. This analysis can serve as a strong decision-making tool to take appropriate actions with respect to the operational conditions to accelerate start up or attainment of near complete nitritation-anammox performance.