Predators are instrumental in structuring natural communities and ecosystem processes. The strong effects of predators are often attributed to their high trophic position in the food web. However, most predators have to grow and move up the food chain before reaching their final trophic position and during this developmental process, their traits, interactions, and abundances change. Here we show that this process of “moving up” the food chain during development strongly determines the ecological role of a predator. By experimentally manipulating the succession of developmental stages of a predatory salamander in seasonal aquatic ecosystem, we found that effects of this apex predator on the ecosystem typically declined with age and size. Furthermore, younger, smaller predator stages had long-lasting effects on community structure and ecosystem function that determined effects of subsequent older, larger stages. Consequently, legacy effects of early stages largely shaped the impact of the predator on the ecosystem, which could not simply be inferred from its final trophic position. Our results highlight that accounting for all life stages when managing natural populations is crucial to preserve functioning of natural ecosystems, especially given that early life stages of species are often particularly vulnerable to natural and anthropogenic disturbances.