Complete Autotrophic Nitrogen Removal (CANR) is a novel process where ammonia is converted to nitrogen gas by different microbial groups. The performance of the process can be compromised by an unbalanced activity of the biomass caused by disturbances or non-optimal operational conditions. This contribution describes the development of a fuzzy-logic based system for both diagnosis and control of a CANR reactor. Based on a combination of measurements of the nitrogen species concentration in the influent and in the effluent on the one hand, and insights into the activities of three distinctive microbial groups on the other hand, the diagnosis provides information on: nitritation, nitratation, anaerobic ammonium oxidation and overall autotrophic nitrogen removal. These four results give insight into the state of the process and are used as inputs for the controller that manipulates the aeration to the reactor. The diagnosis tool was first evaluated using 100 days of real process operation data obtained from a lab-scale single-stage autotrophic nitrogen removing reactor. This evaluation revealed that the fuzzy logic diagnosis is able to provide a realistic description of the microbiological state of the reactor with process engineering insight analysis. An evaluation of both the diagnosis tool and the controller was done by simulating a disturbance in the influent concentration. High and steady nitrogen removal efficiency was achieved thanks to the diagnosis and control system. Finally, development of the diagnosis and control as two independent systems provided further insight into the operation performance, gives transparency towards the operator and makes the system flexible for future maintenance or improvements. (C) 2014 Elsevier Ltd. All rights reserved.