A cell suspension of the nitrifying bacterium Nitrosomonas europaea obtained after 96-h cultivation was subjected to magnetic separation using chitosan-conjugated magnetite particles (chitosan-magnetite), which have the ability to form aggregates with microbial cells. An equilibrium condition was obtained at room temperature after 30 min and over 90% of the cells were recovered when the chitosan-magnetite concentration was 200 mg/l. The relationship between the cell concentration in the supernatant in equilibrium and the number of cells adsorbed per 1g chitosan-magnetite was expressed by a Freundlich-type adsorption equation. A high nitrifying bacterium activity yield was obtained with a chitosan-magnetite concentration between 100 and 200 mg/l. Repeated batch culture resulted in more N. europaea cells accumulating on the aggregates and as a consequence their nitrification activity improved further. The chitosan-magnetite/cell aggregates were recovered and employed to remove ammonia from artificial wastewater together with PVA-alginate gel beads containing the denitrifying bacterium Paracoccus denitrificans. A higher ammonia removal rate was achieved under aerobic conditions in comparison with that obtained when N. europaea and P. denitrificans were coimmobilized in PVA-alginate gel beads.