BackgroundNaphthalene is a polycyclic aromatic hydrocarbon, highly dangerous for human health. It is produced as a byproduct of incomplete combustion of organic material and is frequently present in the air. Biofilters offer an effective alternative for its treatment. The aim of this work was to study the treatment of naphthalene vapors through biofiltration using two biofilters: one inoculated with a consortium composed of Fusarium solani and Rhodococcus erythropolis (BF1), and the other inoculated with a consortium of microbial isolates obtained from a previous biofilter eliminating naphthalene vapors.ResultsThe results demonstrate that inoculating a biofilter with a reconstructed consortium of microbial isolates from a naphthalene vapor‐eliminating biofilter allowed a reduction of the startup time from 35 to 5 days, while maintaining a consistent removal capacity (6 g m−3 h−1, equivalent to 80% removal efficiency). It was also observed that the biofilter inoculated with the reconstructed consortium exhibited comparable robustness to a biofilter previously operated for 4 months with naphthalene, with a maximum removal capacity of 14 g m−3 h−1 for a naphthalene inlet load of 17 g m−3 h−1. The study of microbial communities indicates an increase in the bacterial variability, while fungal variability remains low, with Fusarium solani being predominant at 97%.ConclusionsResults obtained during the startup of both biofilters and by challenging biofilters to increasing naphthalene concentrations or decreasing empty bed residence time showed that startup time can be reduced sevenfold by selecting the microbial consortium. An equivalent performance, in the long run, was achieved for both biofilters. © 2024 Society of Chemical Industry (SCI).