BACKGROUND Methanol vapors, broadly emitted by industry, can be cost‐effectively treated by biofiltration. However, long‐term operation under high concentrations regularly encountered in the pulp and paper industry (> 5 g m−3) has been barely studied. RESULTS Methanol concentrations between 1.6 and 14 g m−3 were treated in a biofilter. Complete methanol removal was obtained for concentrations up to 3.5 g m−3, for an empty bed retention time (EBRT) of 60 s. A higher EBRT (160 s) was necessary to eliminate all methanol for concentrations up to 7 g m−3. For higher concentrations, a maximum elimination capacity (ECmax) of 343.8 g m−3 h−1 was achieved. The main challenge encountered during the biofiltration of high methanol concentrations was excessive biomass buildup (with a performance drop due to clogging occurring every 2 weeks). Under high methanol concentrations, 11 bacteria, three fungi, and one yeast prevailed in the biofilm. Flies and fly larvae were detected when no biofilter clogging was observed, regulating biomass excess. CONCLUSIONS High methanol concentrations trigger biomass growth and clogging. Diptera represent a research opportunity to control such phenomena. © 2019 Society of Chemical Industry