Heavy infestations of a non-indigenous shrub, Amur honeysuckle (Lonicera maackii) are frequently linked to poor individual performance and reduced species diversity. We used chronosequence methods and analysis of forest strata to investigate potential impacts of L. maackii on 1) species richness, 2) density of sub-canopy recruitment layers, 3) indicator species affinity, and 4) within- and among-strata compositional similarities. We compared sites ranging from 12 to 26 years since initial invasion as well as non-invaded, control sites. When assessing non-invaded versus long-invaded sites, we found significantly (P ≤ 0.05) reduced densities in the herb (−57%), seedling (−58%), and sapling layers (−90%), and also reduced species richness in the seedling (−34%), and sapling (−58%), and herbaceous layers (−4%). Interestingly, the germinable seed bank density showed significant increases among non-invaded and long-invaded sites ( 78%), while the species richness of the seed bank demonstrated a marked decrease (−41%). Indicator species analysis found that most species had greater frequencies and abundances in non-invaded sites, and nearly all species had greater affinities for the non-invaded sites, especially in the seedling, sapling, and seed bank layers. Responses were species-specific in the herbaceous layer. Within-layer species similarity decreased with increased time of L. maackii occupancy in all sub-canopy strata. This pattern was also found with reductions in between-layer compositional similarity for the long-invaded (r = 0.16) versus the recently-invaded (r = 0.37) and non-invaded (r = 0.51) sites. Our data suggest that in many invaded sites, habitats are experiencing wholesale alterations in species composition, structure, and successional trajectory, and invasion may also change competitive interactions in forest understories as well as alter between-layer species linkages. These results validate the candidacy of L. maackii sites for increased removal and restoration efforts.