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Ecosystem managers face a difficult decision when managing invasive species. If they use aggressive practices to reduce invader abundances, they will likely reduce invaders' competitive impacts on natives. But it is often difficult or impossible to reduce invaders without damaging natives. So a critical question becomes: Which is worse for native biota, invaders or things done to control invaders? We attempted to answer this question for a common scenario. We studied several grassland natives exhibiting long‐term coexistence with an invader and asked how aggressive management (herbicide use) affected the natives. Whether or not grazing was excluded, one‐time herbicide use made two native forbs exceedingly rare for our entire 16‐year study period. Herbicide also made several other native forbs rare, but only when grazing was excluded, and there is evidence that the dominant invader became more abundant in response to the decreases in native‐forb abundances. Throughout the world, terrestrial and aquatic ecosystems are receiving herbicide applications for exotic‐species control. Some of the applications are doubtless warranted because they target small invader patches or larger areas with virtually no remaining natives. However, other herbicide applications occur where large native populations occur, and our data suggest that these applications can be ill advised. Our cautionary tale is told using an herbicide‐treated grassland, but our results should be considered wherever invasive‐species management damages native species.