Partial migration, where migrant and resident organisms coexist within the same population, has been found in many fishes. Although it seems obvious that different life cycles exploit habitats and food webs differently, few assessments about the trophic consequences of partial migration are available. To unveil part of this complexity, we combined otolith chemistry with stable isotope analyses data for hind-casting Merluccius australis habitat use and diet composition at age. By providing detailed information about lifetime variability in diet, trophic position, and prey demand of four M. australis life-cycle types, we show that these groups feed differentially in estuarine and oceanic habitats throughout their ontogeny. Although trophic positions were similar between habitats for juvenile and subadults, substantial differences between life-cycle types were found regarding lifetime diet and trophic demand. Thus, the more abundant and heavily exploited oceanic stock of M. australis was heavily dependent of estuarine habitats within the Patagonian Fjords System, where it consumes large biomasses of Macruronus magellanicus, Pasiphaea, Sprattus fuegensis, and Euphausiidae at earlier stages. We show ignoring trophic consequences of partial migration and life-cycle diversity may produce highly biased results, both in terms of prey and habitat use, which appears critical for multispecies and ecosystem management approaches.