Eradications of invasive species often have striking positive effects on native biota. However, recent research has shown that species removal in isolation can also result in unexpected changes to other ecosystem components. These secondary effects will become more likely as numbers of interacting invaders increase in ecosystems, and as exotics in late stages of invasion eliminate native species and replace their functional roles. Food web and functional role frameworks can be used to identify ecological conditions that forecast the potential for unwanted secondary impacts. Integration of eradication into a holistic process of assessment and restoration will help safeguard against accidental, adverse effects on native ecosystems.