Pig exhaust air contains a high nitrogen load, mostly as ammonia, and many odorous organic compounds, which are usually low in concentration but can have a significant impact on odor nuisance. Biofiltration of air with biological air scrubbers is frequently used as an effective technique for exhaust treatment of mechanically ventilated animal houses. In this study, the effect of inoculation on the microbial community structure was evaluated. The study was performed with both a three-stage and a two-stage full-scale biological air scrubber system treating pig exhaust air. The two-stage air scrubber was inoculated with thickened activated sludge of a nearby domestic wastewater treatment plant. The bacterial population was monitored during the first three months of the start-up using 16S metabarcoding of samples collected at the different stages of the air scrubbers and in both the biofilm and washing water.