Stumps comprise up to 80% of the residual deadwood following clear cutting and are a significant source of biomass for bioenergetic applications. However, stump harvesting may pose significant conservation risks for saproxylic organisms that occur in residual deadwood. To define retention targets for stump harvesting operations, we compared abundance and species richness of saproxylic beetles within individual stumps as well as species accumulation curves in replicated pairs of clear cuts with and without stump harvesting in northern Sweden. Using 20 stands, we sampled 1049 stumps using eclector traps and collected 9821 beetles representing 253 species with known saproxylic biology. Nineteen of these species were red-listed in Sweden. We hypothesized that individual stumps left following stump harvesting would contain higher densities and species richness than in clear cuts without stump removal due to crowding of beetles into increasingly limited habitats. However, we found no difference in density or richness within individual stumps between control clear cuts and stumped stands. We also compared species richness between control and stumped treatments using rarefaction within individual stands and across all stands and found no difference. As with density and richness, beetle composition at the stand-level did not differ between control and stumped stands. Thus, the density of surrounding stumps within a stand had very little effect on beetle assemblages in residual stumps. We estimated the effect of stump harvest on species richness at the stand level by combining all samples and extrapolating a rarefaction curve derived from the landscape-level species pool to an accumulated sample volume of 48 m3 which corresponds to the total volume of stumps on average-sized clear cuts in Northern Sweden. Using this curve, we compared differences in species richness in average-sized clear cuts with 100% (48 m3) and 25% (12 m3) stump retention and found that stump harvest resulted in a 26% (95% C.I. 7–41%) loss of species. While the absolute scaling of the landscape-derived rarefaction does not reflect species loss at the stand-level because the combined curve reflects all rare species in the landscape, the relative species loss derived from this curve may serve as credible benchmark for species loss at the stand level following current stump harvesting practices. This benchmark may be further calibrated with additional information on number of singleton species and estimates of maximum species richness.