Biological invasions cause many impacts that differ widely in how they are perceived. We argue that many conflicts in the valuation of the impacts of alien species are attributable to differences in the framing of the issue and implicit assumptions—such conflicts are often not acknowledged. We present 13 principles that can help guide valuation and therefore inform the management of alien species. Seven of these relate to the science domain, representing aspects of change caused by alien species that can be measured or otherwise assessed using scientific methods. The remaining six principles invoke values, risk perception, and environmental ethics, but also cognitive and motivational decision biases. We illustrate the consequences of insufficient appreciation of these principles. Finally, we provide guidance rooted in political agreements and environmental ethics for improving the consideration of the consequences of these principles and present appropriate tools for management decisions relating to alien species.