This work aims at investigating the denitrifying P removal activity when nitrite is used as sole electron acceptor in a sequencing batch reactor (SBR) with either acetate or propionate as carbon source. For this aim, biomass withdrawn from a conventional EBPR anaerobic-aerobic system, which had never been exposed to anoxic conditions, was gradually acclimatised to nitrite-based anaerobic-anoxic (A(2)) conditions using propionic acid as carbon source. Once the aerobic phase was suppressed, the denitrifying P removal activity was sustained for more than one month being nitrite the only electron acceptor present. However, when the carbon source was switched to acetate, the system progressively reduced its dephosphatation capacity. The A(2) operation with propionate increased the percentage of PAOMIX-binding cells, while reducing the percentage of DF1MIX. After the A(2) operation with acetate. DF1MIX-binding cells were practically removed of the system, while the PAOMIX percentage was also reduced. The measured decrease in DF1MIX GAO when switching the carbon source could explain the decrease in the glycogen levels during the A(2) operation with acetate. Moreover, the most significant parameters of the EPBR process (P/C ratio, PHA distribution, glycogen production rate, NUR/PUR ratio) under acetate and propionate-fed conditions were compared and discussed. (C) 2010 Elsevier Ltd. All rights reserved.