In Europe, some non-native tree species (NNT) are classified as invasive because they have spread into semi-natural habitats. Yet, available risk assessment protocols are often based on a few limited case studies with unknown representativeness and uncertain data quality. This is particularly problematic when negative impacts of NNT are confined to particular ecosystems or processes, whilst providing valuable ecosystem services elsewhere. Here, we filled this knowledge gap and assessed invasion risks of two controversially discussed NNT in Germany (Quercus rubra L., Pseudotsuga menziesii (Mirb.) Franco) for broad forest types using large scale inventory data. For this purpose, establishment success of natural regeneration was quantified in terms of cover and height classes. The current extent of spread into protected forest habitats was investigated in south-west Germany using regional data. Establishment was most successful at sites where the NNT are abundant in the canopy and where sufficient light is available in the understory. Natural regeneration of both NNT was observed in 0.3% of the total area of protected habitats. In forest habitats with sufficient light in the understory and competitively inferior tree species, there is a risk that Douglas fir and red oak cause changes in species composition in the absence of management interventions. The installation of buffer zones and regular removal of unwanted regeneration could minimize such risks for protected areas. Our study showed that forest inventories can provide valuable data for comparing the establishment risk of NNT amongst ecosystem types, regions or jurisdictions. This information can be improved by recording the abundance and developmental stage of widespread NNT, particularly in semi-natural ecosystems.