Silvicultural disturbance can lead to major shifts in biotic and abiotic characteristics of forests, with significant implications for wildlife. Many studies have demonstrated site occupancy and abundance of small mammals changes following silviculture, but few have identified the habitat characteristics associated with small mammal responses. We conducted a study in the central hardwood forest region of the U.S. to examine the relationship between small mammal habitat use and habitat variables at the microsite scale, before and after silvicultural disturbance, while explicitly accounting for imperfect detection. Following the creation of harvest openings, vegetation cover and coarse woody debris increased, and leaf litter depth decreased. Fewer changes occurred following the midstory removal stage of a shelterwood harvest. Eastern chipmunks (Tamias striatus) and white-footed mice (Peromyscus leucopus) were positively correlated with woody vegetation cover and coarse woody debris, and short-tailed shrews (Blarina brevicauda) were positively correlated with coarse woody debris and leaf litter depth. Careful consideration of experimental scale and incorporation of detection probability are necessary for successful identification of small mammal associations within microhabitats, as these relationships help to explain shifts in small mammal communities following silviculture.