The performance of a full-scale biotrickling system for the treatment of exhaust gases from two different paint sources at a furniture facility, was investigated applying Fluorescense in situ hybridization (FISH). This technique allowed the detection of major bacteria groups and, therefore, helped in understanding complex microbial communities. The results indicated that Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria were more predominant than Firmicutes and Actiniobacterias. In addition, a variation in the composition of the bacterial community throughout the time of operation and with the paint source was observed. Betaproteobacteria showed similar relative abundance in all analyzed days. However, Gammaproteobacteria, relevant group in the degradation of VOCs, fluctuated with operational changes and the relative abundance of Alphaproteobacteria decreased when the composition of pollutants of the emission source was changed.