Abstract Autotrophic domestication for short-cut nitrification (SCN) and microorganism immobilization was carried out in a lab-scale biological aerated filters (BAFs) system with activated sludge. Zeolite was chosen as fillings and modified to enlarge the specific surface and to remove toxic metal ions. After thirty-day domestication and immobilization, the NH4+-N removal capacity increased to 76.51mg/g dry sludge (DS) and the ratio of NO2--N converted from NH4+-N reached to 91.2% finally. The analysis of growth kinetics indicated that free ammonia should be the key factor for SCN. The abundance variation of nitrifiers, measured by qPCR, showed that AOB was enriched successfully and NOB was washed out. The results also showed that modified zeolite should be more beneficial to the specific immobilization of AOB than natural zeolite. The shift in the community structure of AOB during the domestication by DGGE profile was investigated.