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A diversity of microhabitats has been suggested to play a key role in mediating the co-occurrence of trees with specific tree-inhabiting biodiversity, which may further influence ecosystem functioning. However, this triple relationship between tree characteristics, tree-related microhabitats (TreMs), and biodiversity has not been described explicitly enough to set quantitative targets of ecosystem management. The two major approaches directly targeting TreMs in ecosystem management are tree-scale field assessment of TreMs and precautionary management, which both require insights into the predictability and magnitude of specific biodiversity-TreM relationships. To obtain such insights, we analysed tree-scale relationships between the diversity of TreM development processes (four classes: peculiarity; pathology; injury; emergent epiphyte cover) and selected biodiversity variables based on 241 live trees (age range 20–188 years) of two species (Picea abies , Populus tremula) in hemiboreal forests in Estonia. We addressed the diversity and abundance of epiphytes, arthropods, and gastropods; their specific response to TreMs was disentangled from tree age and tree size effects. We found that a relatively small improvement in the biodiversity responses studied was attributable solely to TreMs, and that such contribution was more frequently observed in young trees. Unexpectedly, several age- or size-independent effects of TreMs were negative, suggesting trade-offs with other factors of biodiversity relevance (such as tree foliage suppression due to injuries that created TreMs). We conclude that tree-scale microhabitat inventories have only limited potential to resolve the general problem of providing diverse habitats for biodiversity in managed forests. The basic sources of uncertainty are that microhabitat management is mostly indirect (managing TreM-bearing trees and stands rather than TreMs themselves) and that snapshot surveys cannot address various time perspectives. We outline a set of basic principles and constraints for spatially heterogeneous and precautionary forest management that includes TreM diversity considerations. These principles can be further elaborated through multi-scale research on functional biodiversity links of TreMs. [Display omitted] • Established conservation approaches do not directly address the microhabitat scale. • We studied tree-related microhabitats (TreMs)–biodiversity links in Estonia. • TreMs had weak, sometimes negative effects, after accounting for tree age and size. • TreMs do not form a distinct conservation approach, but can specify those existing. • Spatial heterogeneity and precautionary approach in forest management recommended. [ABSTRACT FROM AUTHOR]