A membrane inlet mass spectrometer (MIMS) was used in combination with a developed computer model to study and improve management of a biofilter (BF) treating malodorous ventilation air from a meat rendering facility. The MIMS was used to determine percentage removal efficiencies (REs) of selected sulfur gases and to provide toluene retention profiles for the model to determine the air velocity and overall mass-transfer coefficient of toluene. The mass-transfer coefficient of toluene was used as a reference for determining the mass transfer of sulfur gases. By presenting the model to scenarios of a filter bed with a consortium of effective sulfur oxidizers, the most likely mechanism for incomplete removal of sulfur compounds from the exhaust air was elucidated. This was found to be insufficient mass transfer and not inadequate bacterial activity as anticipated by the manager of the BF. Thus, knowing the relationship between mass-transfer coefficients and air velocity for a given type of BF allows for an improved dimensioning and managing of this and similar BFs. This research demonstrates that it is possible to estimate mass-transfer coefficients and air velocity in BFs using MIMS in combination with computer modeling.