Conservation planning addresses the development and expansion of protected areas and requires data on for instance species, habitats, and biodiversity. Data on threats is often minimal, although necessary in conservation planning. In principle, threats should guide which conservation actions to take and where, and how to allocate resources. The lack of threat information may also limit the validity of areas to be conserved, if the condition of areas is degraded by threats unknown. The protocol described here outlines the methodology for a systematic review to explore how threats are theoretically and methodologically understood and used in conservation plans across freshwater, marine and terrestrial environments. Our primary research question is: how have threats informed conservation planning? Studies will be categorized according to the types of threats and conservation features used, theoretical and methodological approaches applied, geographical context, and biome. The results are expected to increase our understanding about how threats can and should be addressed in conservation planning.