Project prioritization protocols are an important tool for allocating conservation resources efficiently, and have been applied to a range of species and ecosystems. Current approaches are inadequate when applied to species with distinct threats impacting different and/or multiple life history stages, such as sea turtles. We develop a model that integrates the benefit of any management project on a population by way of its expected population growth rate, including projects targeting different and/or multiple life history stages. To illustrate its utility, we prioritize projects for investment relevant to Australia's eastern population of Flatback turtle (Natator depressus). We rely upon expert‐elicitation to estimate individual benefit parameters, feasibility, and cost, and calculate the cost‐effectiveness of each project. The most cost‐effective project was not the most feasible, cheapest, or most beneficial. Our approach will help managers make efficient decisions that account for the full range of threats operating on a population.