Phosphorus is both a major environmental pollutant and a limiting resource. Although enhanced biological phosphorus removal (EBPR) is used worldwide for phosphorus removal, the standard activated sludge-based EBPR process shows limitations with stability and efficiency. Recently, a new EBPR moving bed biofilm reactor (MBBR) process has been developed at HIAS (Hamar, Norway), enabling a phosphorus removal stability above 90% during a whole year cycle. To increase the knowledge of the HIAS (MBBR) process the aim of the current work was to characterize the MBBR microbiota and operational performance weekly for the operational year. Surprisingly, we found a major succession of the microbiota, with a five-fold increase in phosphorus accumulating organisms (PAOs), and major shifts in eukaryote composition, despite a stable phosphorus removal. Temperature was the only factor that significantly affected both phosphorus removal and the microbiota. There was a lower phosphor removal during the winter, coinciding with a higher microbiota alpha diversity, and a lower beta diversity. This differs from what is observed for activated sludge based EBPR. Taken together, the knowledge gained from the current microbiota study supports the efficiency and stability of MBBR-based systems, and that knowledge from activated sludge-based EBPR approaches cannot be translated to MBBR systems.