Woody debris provides substrate for a large part of forest biodiversity. Many saproxylic species are threatened by deadwood removal from commercial forests. However, deadwood availability alone may be insufficient to sustain those specialist species, given that naturally they inhabit diverse and dynamic forest ecosystems. We analysed the occurrence of saproxylic beetles under the conditions of semi-natural forestry in Estonia where managed stands are relatively rich in deadwood. We had two aims: (i) to estimate the role of deadwood amount taking into account other habitat factors for the beetles, and (ii) to contribute to the assessment of ecological sustainability of the silvicultural approaches used. The 128 studied stands represented four management stages: clear-cuts, retention cuts with solitary trees, mature commercial forests, and (as reference) old growth across a gradient of forest site-types. Using flight-intercept traps and rearing from wood samples, we captured 105 pre-defined habitat specialist species, of which 41% were of regional conservation concern. Site-scale occurrence of 34 species modelled for habitat factors depended mostly on management stage and forest type. Harvested sites (particularly retention cuts) were primarily preferred, and dry pine sites had a distinct fauna. Thirteen percent of target species favoured old growth, but in general, the beetle assemblages in old growth resembled those in mature commercial forest. Statistical significance of any stand characteristics (site type; stand structure) was established in only 62% of species, which indicates that there can be additional important factors, such as habitat connectivity, patch size or landscape history. These results highlight the importance of diverse forest management and protection approaches for deadwood-dwellers, which should aim for habitat heterogeneity along with substrate diversity. For beetle diversity, retention cutting performs much better than clear-cutting, but even deadwood-rich mature stands cannot fully substitute old growth. We conclude that deadwood abundance serves only as a starting consideration for reconciling timber production and the conservation of deadwood dependent biodiversity.