Biofiltration is economic biotechnology of high efficiency for the removal of odorous gases, such as hydrogen sulphide (H2S) and ammonia (NH3), produced in different activities such as wastewater treatment plants (WWTP). However, in the case of H2S and NH3 treatment, the fluctuations in the concentration of gases found in industrial emissions and the accumulation of oxidation products in the biofilter bed can affect the elimination efficiency. Considering this disadvantage, in this work, we evaluated the performance of compost biofilters inoculated or uninoculated with a microbial culture enriched in nitrifying and sulphur-oxidizing bacteria (SOB) for the removal of H2S and NH3 under transient conditions of concentration, simulating industrial operation. The compost bed was made from chicken manure and sugar cane bagasse, and the biofilter operating conditions were: 1) empty bed residence time of 25 s and 2) bed moisture of 40%. The gas concentration and transient conditions simulated the emissions of H2S and NH3 in the pre-treatment zone of a WWTP during the dry and rainy season in Bogota, Colombia. The biofiltration performance was evaluated considering the removal efficiency and oxidation products (sulphate, nitrate and ammonium). The biofilters had a 100% removal efficiency for both gases during the rainy season and transition stages. However, the H2S and NH3 oxidation was affected by the daily changes in gas concentration. The increase of gases concentration at the last week of the dry season resulted in a gradual decrease of H2S and NH3 removal efficiency for both biofilters. However, the reduction in the removal efficiency was higher in the uninoculated biofilter. In addition, there was a higher increase in nitrate concentration in the inoculated biofilter. These results indicate that the inoculated biofilter could adapt better to the transient conditions of gas concentration.