In this study, a pilot-scale two-stage denitrification filter (TSDNF) was developed to further remove the effluent nitrate from a cyclic activated sludge system. Sponge iron and volcanic rock were used as DNF-1 and DNF-2 filter beds, respectively. A single-stage DNF-3 filter with volcanic rock was used as the control. Most dissolved oxygen (DO) was consumed for iron oxidation in the DNF-1, and in turn denitrification rates increased in the DNF-2. In the DNF-1, 17.9 %±13.6 % of the NO3−-N was removed in the absence of organic carbons, resulting in a significant increase in the total NO3−-N removal in the TSDNF with a COD/NO3−-N ratio of about 2.6. Autotrophic denitrification should be finished by the dominant Fe(II)-oxidizing nitrate-reducing Gallionellaceae genus (21.38 %) in the DNF-1, while common denitrifying strains were dominant in both DNF-2 and DNF-3. Moreover, obvious chemical phosphorus removal (83.3 %) was found in the DNF-1. Therefore, simultaneous autotrophic denitrification and chemical P-removal can be achieved using iron ions released from sponge iron filters, which provides a new model to reshape the design of advanced removal of nitrogen and phosphorus in the secondary clarifier effluent.