A pilot-scale bio-trickling filter (BTF) packed with ceramsite was investigated to treat butan-2-yl ethanoate (BE), which is discharged from the pharmaceutical industry. To choose an appropriate operation technology, the performance of twin bench-scale BTFs, vertical (BTF1) and horizontal (BTF2) towers, to purify BE were tested. The BTF1 had superior degradation capabilities when compared to BTF2, a quick start up of three days, a maximum elimination capacity of 548.5 g/(m(3)h) and an average removal efficiency of approximately 95% with an empty bed residence time (EBRT) of 17 s. Therefore, in a subsequent pilot test, a vertical BTF with a high temperature shade net was setup, which demonstrated effective BE degradation performance. The pressure drop of the vertical BTFs could be addressed effectively by commutation and optimizing the nutrient supply. A high-throughput sequencing comparison of the three towers indicated similarity in the microorganisms between the two vertical BTFs, indicating that the flow patterns within the tower could affect microorganisms cultivation.