The use of silvicultural systems based on the natural disturbance patterns for a given region has been suggested as an approach for promoting late-successional forest characteristics and maintaining native biodiversity in managed forests. To this end, we examined the effectiveness of natural disturbance-based harvest gaps in maintaining and restoring native tree species diversity within second-growth northern hardwood systems in northeastern Minnesota, USA. In particular, tree regeneration and downed coarse woody debris (CWD) were measured 6- and 7-years post-treatment in 46 gaps that emulated the historic range of natural canopy opening sizes for northern hardwood forests in the upper Great Lakes region. Measurements were compared across gap size-classes (>0–0.02, >0.02–0.04, >0.04 ha) and with closed canopy portions of these systems. In addition, the factors affecting the recruitment of Betula alleghaniensis across gaps and within closed canopy were investigated due to the historical importance of this species in these forests. Seedling and sapling densities increased in harvest gaps; however, results indicated that these gaps did little to increase tree diversity, including the recruitment of shade mid-tolerant species, such as B. alleghaniensis. Gaps were dominated primarily by Acer saccharum and age distributions of dominant saplings within gaps indicated that most individuals established 10–40 years prior to gap formation. Establishment of B. alleghaniensis was strongly related to highly decayed, large coniferous pieces of CWD with little recruitment occurring on the undisturbed forest floor. Age distributions of B. alleghaniensis established on CWD suggest this species can persist on this substrate for at least a decade. Levels of CWD increased with increasing gap size; however, all gaps had lower levels of CWD compared to the surrounding intact forest. Our results suggest that management regimes based on natural canopy gap sizes within northern hardwood systems will do little to restore native tree diversity if provisions for creating the suitable seedling microsites historically generated by natural disturbance (e.g., exposed mineral soil, highly decayed wood) are not included within management prescriptions.