Management of invasive plants is often justified in terms of protecting native communities. However, for the vast majority of introduced species, understanding of interactions with and impact on our native flora and fauna is limited. Outcomes of management of invasive species for native communities is similarly poorly understood. Simultaneously, co-occurring stressors challenge our ability to determine drivers of change and assess impacts. Here, we employ a framework using native plants as indicators to understand the impacts of invasive plants and their management. We share two case studies assessing: 1) impacts of Brachypodium sylvaticum, a low abundance and low information species, on native understory forest plants in New York, and 2) how the legacy of invasion and management of Phragmites australis in Adirondack wetlands influences native plants. In our first study, we found species-specific, but overall negative responses of plants to B. sylvaticum presence and generally positive responses to protection from deer, with limited interactions between the two. In the second study, we found site and species-specific responses to growing conditions, with plants able to survive and grow in previously treated areas, suggesting the legacy of P. australis management did not permanently limit plant re-establishment in wetlands. Taken together, using native plants as indicators (transplanting and monitoring desirable plant species) can be a powerful approach to understand and quantify both impacts of invasive species and non-target impacts, while accounting for other stressors.