Lipophilic extractives naturally occurring in wood tend to coalesce during pulping to form pitch deposits, which have particularly undesirable effects on the pulping process and quality of pulp produced. A chemical characterization of different eucalypt species [Eucalyptus nitens, E. grandis, and E. dunnii (of different site qualities)] wood and generated pulp was performed. This study aimed at determining the effects of wood storage at -20 °C (for 6 months), by examining their chemical composition and indigenous microflora. Fatty acids were the main lipophilic compounds among E. dunnii (SQ3 and SQ4) and E. grandis wood extractives. The wood of E. nitens posed the least risk for pitch deposit formation, making it the most suitable Eucalyptus species for pulping. Storage of wood chips at -20 °C had a similar effect as the traditional method of seasoning (storage of wood outdoors prior to pulping) used for the reduction of lipophilic extractives. A 25 to 44% reduction of total extractives was observed in the raw material after storage. Variations in bacterial and fungal communities were observed after storage, and should be taken into consideration when conducting lab scale trials. If storage of wood chips is necessary for lab testing, it should be retained for a maximum of 3 months at -20 °C.