Physiology and behaviour are closely linked, making knowledge of the interaction between species’ energetics and activities important when attempting to understand how animals function in the wild. I examined torpor use by western pygmy-possums (Cercartetus concinnus) and eastern pygmy-possums (C. nanus) in relation to nest site characteristics and movement patterns. In coastal mallee heath in winter, C. concinnus nested beneath leaf litter at the base of dead Banksia ornata, where they employed torpor on 69% of observed days. In warm temperate sclerophyll forest, C. nanus nested in tree hollows of Eucalyptus spp. and used torpor on 64% of days in winter and 10% in summer. Torpor was used in nest sites that were buffered from outside temperature extremes. Both species frequently reused nest sites and while C. nanus was more likely to employ torpor in a previously used site, site familiarity did not influence torpor use for C. concinnus. Additionally, C. nanus was more likely to use torpor in hollows with a higher relative thickness in both seasons. No relationship was found between range size and the number of tracking days or capture body mass, though sample sizes were small. I suggest that the thermal attributes of nest sites influence torpor use for both species and this is likely vital for maintaining a positive energy balance, stressing the importance of preserving habitat with ample potential nest sites for conservation management.