Changes in the number and species diversity of cultivable microorganisms in a newly developed plate-type biofilter during filtration of various volatile pollutants were studied. The novelty of the investigation is the monitoring of microorganism succession in different parts of biofilter plates with original packing material consisting of birch fibre and needle-punched non-woven fabric. It was shown that the largest number of fungi and yeasts develop on the top and middle, while bacteria develop on the bottom and middle parts of plates. The number of microorganisms depends on the origin of the pollutant, the pH and temperature inside the biofilter and the moisture of the porous plates. The statistically significant correlation between the number of microorganisms and inlet concentration of acetone was estimated, while ammonia showed a negative influence on yeast distribution. Paecilomyces variotii, Rhodotorula mucilaginosa and Bacillus subtilis were the most common organisms found during filtration of all examined volatiles; however, some differences of microbial communities in different parts of the biofilter plates and filtrated volatile compounds were obtained.