Rock glaciers and other forms of blocky debris underlain by permafrost or seasonal ice often serve as habitat for iconic montane species such as marmots, pikas and pine martens, as well as many smaller animals forming the montane prey base. This microhabitat offers relatively cool refuge during the summer and is commonly insulated by snow cover during the winter. The American pika (Ochotona princeps) is known to use these microhabitats to shed heat during the summer and to escape extreme temperatures year-round. However, little is known about how these sub-surface microclimates vary with surface features and microhabitat structure. We used a comparative approach to characterize sub-surface temperatures in blocky debris relative to aspect, elevation, debris depth, canopy cover, sub-surface water flow, and interstitial cavity size (indexed by rock/clast size). Data loggers were placed in “shallow” (<10 cm) and “deep” (>50 cm) sub-surface positions to record temperatures during 2013-2014 at sites on and adjacent to Niwot Ridge in Boulder County, Colorado, USA. In shallow positions during winter, average temperatures in a talus patch were significantly warmer toward patch edges, and significantly colder at higher elevations and on north-facing slopes. During summer, average temperatures in deep cavities showed no significant effect of aspect, but declined significantly with increasing elevation at a sub-surface lapse rate of nearly 1°C per 100 vertical meters. Excluding shallow placements, average temperatures declined significantly with cavity depth, at almost 6°C per meter. Canopy cover had a moderating effect on temperature in shallow cavities, and sub-surface water flow moderated temperature in deep cavities. Finally, the difference and lag in temperature between shallow and deep cavities declined with clast/cavity size. On a daily basis, the lag between surface and sub-surface temperatures in blocky debris should affect the potential for small animals to use these microhabitats for efficient thermoregulation. At larger timescales, the lag between surface and sub-surface temperatures in blocky debris should affect the persistence of sub-surface water resources.