The African penguin population has declined precipitously in recent decades, and if current rates of decline persist, this species could become extinct in the wild by 2035. Resource extraction of small pelagic fish prey by the purse-seine fishery around African penguin breeding colonies has been identified as a demographically meaningful threat to African penguins. Consequently, long-term, effective no-take zones around breeding colonies have been endorsed by an expert panel of scientists constituted by the South African government. Here, we consider the six largest South African penguin colonies that currently hold 76% of the global population. We evaluate the adequacy of different no-take zone options using a trade-off mechanism recommended by the expert panel. For all six colonies except Bird Island, Algoa Bay, which is subject to the least fishing pressure, the current no-take zone delineations are assessed as having little benefit to the African penguin and little to no cost to the purse-seine fishery. Four of the six current no-take zones include ≤50% of the African penguins’ core foraging areas. Alternative no-take zones that approximate a more balanced trade-off offer more impactful alternatives to the current fisheries restrictions. Given the urgent need to implement evidence-based conservation interventions for the endangered African penguin, we recommend the substitution of the current no-take zones with those proposed herein.