We aimed to quantify the effects of anthropogenic disturbances on forest structure and diversity in deciduous and mixed boreo-nemoral stands, conditioned on potential confounding factors. Based on these results, we created a statistically-supported indicator list of stand “naturalness”. We surveyed 50 quantitative and qualitative characteristics of a stand, the understorey and forest floor, and several widely accepted biodiversity indicators in 171 forests in Estonia. Multi-factorial GLM and GLIM analyses showed that many forest structural characteristics were confounded by forest site-type specificity, stand age and/or biogeography. Near-natural old-growth forests had higher proportions of deciduous trees, a larger amount of coarse woody debris, a higher frequency of logs in each decay class, a denser understorey, and were more homogeneous in the horizontal pattern of each layer than mature managed forests. By improving light conditions, forest management indirectly increased herb layer richness and coverage and the proportion of graminoids. The critical easy-to-apply set of indicators to assess forest ecosystem quality includes the amount and type of dead wood, the canopy closure of a stand and the presence of specially-shaped trees, specific epiphytic indicator lichens, mosses and wood-dwelling insects, and forest site-type specific herb layer species.