Spatial representations of threatening processes – “threat maps” – can identify where biodiversity is at risk, and are often used to identify priority locations for conservation. In doing so, decision makers are prone to making errors, either by assuming that the level of threat dictates spatial priorities for action or by relying primarily on the location of mapped threats to choose possible actions. We show that threat mapping can be a useful tool when incorporated within a transparent and repeatable structured decision-making (SDM) process. SDM ensures transparent and defendable conservation decisions by linking objectives to biodiversity outcomes, and by considering constraints, consequences of actions, and uncertainty. If used to make conservation decisions, threat maps are best developed with an understanding of how species respond to actions that mitigate threats. This approach will ensure that conservation actions are prioritized where they are most cost-effective or have the greatest impact, rather than where threat levels are highest.