Stumps and slash resulting from forest clearcutting is used as a source of low-net-carbon energy, but there are concerns about the consequences of biofuel extraction on biodiversity. Logging residues constitute potentially important habitats, since a large part of forest biodiversity is dependent on dead wood. Here we used snapshot field data from a managed forest landscape (25 000 ha) to predict landscape scale population changes of dead wood dependent organisms after extraction of stumps and slash after clearcutting. We did this by estimating habitat availability for all observed dead wood-dependent beetles, macrofungi, and lichens (380 species) in the whole landscape. We found that 53% of species occurred in slash or stumps. For most species, population declines after moderate extraction (≤30%) were small (<10% decline) because they mainly occur on other dead wood types. However, some species were only recorded in slash and stumps. Red listed species were affected by slash and stump extraction (12 species), but less often than other species. Beetles and fungi were more affected by stump extraction, while lichens were more affected by slash extraction. For beetles and lichens, extraction of a combination of spruce, pine and birch resulted in larger negative effects than if only extracting spruce, while for fungi tree species had little effect. We conclude that extensive extraction decreases the amount of habitat to such extent that it may have negative consequences on species persistence at the landscape level. The negative consequences can be limited by extracting only slash, or only logging residues from spruce stands.