Assessment of biofiltration systems under transient conditions is necessary when determining industrial operating conditions of biofiltration beds. The key system variables such as filter bed moisture content, the pollutant type and its concentration, must be evaluated in order to accurately calculate scaling of biofiltration beds. The removal efficiency of two organic volatile compounds (VOCs) was evaluated: acetic acid (hydrophilic) and pentane (hydrophobic). Two independent biofiltration systems were operated (A and B), in each system the bed packing material was the same. The filtration beds were made from compost, with the following mixtures: rice husk-chicken manure (CAS) and pruning waste-chicken manure (POD), each in a ratio of 1:1 (v:v). As part of this study, in system A, the effect of moisture on acetic acid removal efficiency was analyzed, finding that in a moisture range of 50-15% and of 50-25%, efficiencies above 90% are reached for CAS and for POD respectively. On the other hand, in system B, the performance of the biofilters was evaluated against different concentrations of pentane, resulting in removal efficiencies of 25% and 43% for POD and CAS, respectively. In general, these results indicate that there is a significant dependence between the performance of the system and the moisture content of the filter bed and the lower limit in which the bed would operate under industrial conditions is defined. The pollutant water solubility was also considered in order to define the maximum concentrations that the bed would support under transient conditions.