Regional systematic conservation planning is an effective approach to marine protected area (MPA) network design, ensuring complementarity, and functional connectivity of areas. However, regional planning and local conservation actions do not properly inform one another. One outcome is the failure of regional designs to guide conservation actions. Another is that site-based MPAs constitute collections rather than functional systems for marine conservation. Understanding decisions related to spatial scale in conservation planning is essential for the development of ecologically functional networks of MPAs. Decisions about scale require that planners address trade-offs between the respective advantages and limitations of different considerations in several parts of the planning process. We provide the first comprehensive review of decisions about spatial scale that influence planning outcomes. We illustrate these decisions and the trade-offs involved with planning exercises undertaken in the Coral Triangle. We provide a framework in which decisions about spatial scale can be made explicit and investigated further. The framework helps to link theory and application in conservation planning, facilitates learning, and promotes the application of conservation actions that are both regionally and locally significant.