•We developed a system for assessing ecological integrity of managed forests.•Focal species link variability in forest condition and habitat to ecological processes.•We found some ecological differences from expected natural conditions.•Results provide insights into why undesirable effects are occurring.•The assessment approach can contribute to evidence-based policy analysis. Ecological integrity of managed forests includes the ability of an ecosystem to support a community of organisms with a similar species composition and functional organization as found in nearby natural systems. We developed an indicator system for ecological integrity based on simulated natural disturbance and indicator species to test if forest condition and habitat in managed forests are similar to that found or expected in natural systems. We then applied the method in an area of the boreal forest (Ontario, Canada) where the objective of Ontario's strategic forest management planning approach is, in part, to conserve ecological integrity through the emulation of the natural disturbance process. Forest condition controls the supply of habitat to support the diversity of native organisms, and historically in boreal forests the natural disturbance process drove forest condition. We selected indicators of forest condition (landscape pattern and compositional mosaic) and habitat function (occupancy rates for a broad range of forest birds), and applied our assessment system to test whether indicators of forest condition and habitat function reflect outcomes expected if natural disturbance processes were successfully emulated. We collected occupancy data in natural and managed forest disturbance types using autonomous acoustic recorders, applied occupancy/detection modeling to estimate corrected occupancy rates (ψ), and then tested for differences in ψ between disturbance types. Some indicators of forest condition were within the range expected under natural disturbance, but we found relatively less old conifer, more young deciduous and greater edge density in managed forests relative to forests of natural disturbance origin. Most species (11 of 14) occurred with equal ψ in habitat originating from the two disturbance types. Brown creeper (Certhia americana), bay-breasted warbler (Mniotilta varia) and red-eyed vireo (Vireo olivaceus) differed between disturbance types. Brown creeper uses older conifer and occurred at lower rates in managed forest, while red-eyed vireo uses a range of deciduous forest ages, and occurred at higher rates in managed forest. Differences in quantity and/or quality of specific habitat types likely explain the responses. The results suggest what directional changes in the forest pattern and compositional mosaic would improve ecological similarity with natural systems, but also indicate what further research is required. We believe this approach to assessing ecological integrity can be adapted to study the effectiveness of conservation management strategies in other systems, and will contribute to adaptive management approaches and evidence-based policy development.