A two-stage exhaust air treatment system installed at a broiler fattening facility with 40,000 animals was investigated. The facility’s exhaust air was treated first by use of a chemo-scrubber (stage 1) and afterwards by a vertical biofilter (stage 2). The biofilter was equipped with root wood and honeycombed paper pad layers (half/half) to enable a direct comparison of both filter materials’ suitability. Odour samples were taken on site and afterwards analysed at an olfactometry laboratory. Ammonia concentration values were collected continuously using a photoacoustic multi-gas monitor. High mitigation performance was achieved with both filter materials, with the honeycombed paper pad layer being less susceptible to fungal growth than the root wood filter. Cellulose seems to be a proper alternative for use in biofilters, but further research is needed to estimate the long-term stability of this material.