Tree-related Microhabitats (TreMs) are of prime concern for biodiversity since they host thousands of taxa. TreMs are discrete habitat patches borne by trees and cover a wide range of lifespans, from days to decades to centuries. The taxa associated with such discrete and sometimes highly ephemeral habitat patches are likely to be sensitive to spatial distribution because they need to search for new habitats after the occupied one disappears. Although many studies have recently been dedicated to TreMs, only very few have investigated their spatial distribution. Focusing on European beech-dominated forests, we used a European TreM database with 12,362 trees and 296 plots (ranging from local (0.1–1 ha) to landscape scale (10,000 ha)) to assess TreM spatial distribution patterns in long unmanaged forests. Then, with a TreM sub-database with 6828 trees and 21 plots, we assessed whether and if so, how harvesting changes spatial patterns at the plot scale. In long unmanaged forests, most TreMs showed a regular pattern at the plot scale and an aggregated pattern at larger scales. Tree diameter was the most influential factor for spatial patterns in TreMs. Spatial patterns at the plot scale in harvested forests differed slightly from those observed in unmanaged forests. To favor TreM-dwelling taxa in harvested stands, our results suggest retaining habitat trees in a regular spatial pattern to mimic the natural pattern. However, some TreMs should be conserved in an aggregate pattern; we specify the spatial scale at which this should be done.