A variety of ecological systems around the world have been damaged in recent years, either by natural factors such as invasive species, storms and global change or by direct human activities such as overfishing and water pollution. Restoration of these systems to provide ecosystem services entails significant economic benefits. Thus, choosing how and when to restore in an optimal fashion is important, but has not been well studied. Here we examine a general model where population growth can be induced or accelerated by investing in active restoration. We show that the most cost-effective method to restore an ecosystem dictates investment until the population approaches an ‘economic restoration threshold’, a density above which the ecosystem should be left to recover naturally. Therefore, determining this threshold is a key general approach for guiding efficient restoration management, and we demonstrate how to calculate this threshold for both deterministic and stochastic ecosystems.