During biomass storage, some gases can be produced and reach dangerous levels to human health. Among them, carbon monoxide is especially worrying, due to its potentially lethal effects and its contribution to the greenhouse effect. High levels of this gas could be reached, depending on many factors, such as unsuitable ventilation in storage areas or raw material characteristics. The aim of this research study was to assess the levels of CO produced during pellet storage at a laboratory scale, depending on the ventilation conditions (changing the amount of sample and frequency), the pellet characteristics (eucalyptus and cork residue pellets), and variables that influence CO levels. A greater number of pellets (when not ventilated) increased CO levels and discontinuous ventilation did not reduce these levels once the space was isolated again. Cork samples provoked higher CO emissions, possibly due to its higher fat content and surface area, which promotes the interaction between air and fatty acids (that is, the auto-oxidation of the samples and the subsequent release of CO). Consequently, continuous and good ventilation is required, especially until CO production from wood auto-oxidation is complete.