Glaucomys sabrinus fuscus (Virginia Northern Flying Squirrel; VNFS) is a rare Sciurid that occurrs in the Allegheny Mountains of eastern West Virginia and northwest Virginia. Previous work on this subspecies has confirmed close associations with Picea rubens (Red Spruce) at the landscape and stand levels in the region. However, ongoing Red Spruce restoration actions using canopy-gap creation to release single or small groups of trees requires a better understanding of within-stand habitat selection of VNFS to assess potential short- and medium-term impacts. To address these questions, we conducted a microhabitat study using radio-collared squirrels in montane conifer and mixed conifer—hardwood stands. We used points obtained from telemetry surveys and randomly generated points within each squirrel's home range to compare microhabitat variables for 13 individuals. We found that VNFS preferentially selected plots with conifer-dominant overstories and deep organic-soil horizons. VNFS avoided plots with dense Red Spruce regeneration in the understory in stands with hardwood-dominated overstories—the types of areas targeted for Red Spruce restoration. We also opportunistically searched for hypogeal fungi at telemetry points and found 3 species of Elaphomyces during our surveys. Our results indicate that microhabitat selection is associated with Red Spruce-dominant forests. Efforts to restore Red Spruce where hardwoods dominate in the central Appalachians may improve the connectivity and extent of habitat of VNFS.