Nitrifiers are the slowest growing bacteria used in conventional biological wastewater treatment. Furthermore, their growth rate is seriously hampered by low temperature. As a result, the volume needed for nitrification dominates the volume of the biological reactors at a wastewater treatment plant. As a way of enhancing nitrification and reducing this volume, bioaugmentation can be used. Nitrifiers from a side-stream plant can be inoculated to the mainstream process, which is thereby boosted. The effect of bioaugmentation can be measured in different ways. This full-scale study focuses on the effect of bioaugmentation from a microbial point of view by using 16S rRNA amplicon sequencing. The study reveals how bioaugmentation increases the diversity of nitrifiers in the mainstream process and in the side-stream plant; that the abundance of nitrifiers is increased in the mainstream process; the interaction between nitrifiers from the side-stream plant and mainstream process; and the effect of bioaugmentation on nitrifying genera and species over time. To our knowledge, this detailed microbial information on nitrifying species during a full-scale bioaugmentation study has not been presented before.