Ecosystem-based management is costly. Therefore, without rigorously showing that it can outperform traditional species-focused alternatives, its broad-scale adoption in conservation is unlikely. We present a large-scale replicated and controlled set of whole-lake experiments in fish conservation (20 lakes monitored over 6 years with more than 150,000 fish sampled) to examine the outcomes of ecosystem-based habitat enhancement (coarse woody habitat addition and shallow littoral zone creation) versus a widespread, species-focused alternative that has long dominated fisheries management practice (i.e., fish stocking). Adding coarse woody habitats alone did not, on average, enhance fish abundance, but creating shallow water habitat consistently did, especially for juvenile fish. Species-focused fish stocking completely failed. We provide strong evidence questioning the performance of species-focused conservation actions in aquatic ecosystems and instead recommend ecosystem-based management of key habitats.