Abstract Many fished stocks show long-term reductions in adult body size. Such changes could lead to new feeding interactions and alter stock productivity, introducing new levels of uncertainty in fisheries management. We use a marine ecosystem model parameterized for Southeast Australia to explore how reductions (up to 6% in 50 years) in size-at-age of fished species affect stock recovery after an implementation of a fishing moratorium. We show that reduction in body size can greatly elevate predation mortality and lower the post-fishing biomass of affected species. In our simulations, the recovery period after the fishing moratorium was characterized by two phases. In the initial readjustment phase, the ecosystem dynamics was largely determined by the rapid changes in the biomasses of recovering species and changes in body size had negligible effects. In contrast, fish body sizes had the major impact on the biomasses in the second, semi-equilibrium state and the final biomasses were generally not affected by the harvest rate during the fishing period. When reduced size-at-age elevated predation mortality in most age groups of a species (tiger flathead Platycephalus richardsoni or silver warehou Seriolella punctata in our simulations), the species' equilibrium biomass was considerably lower compared with the scenarios of no change in body size. For other species (pink ling Genypterus blacodes and jackass morwong Nemadactylus macropterus), a predation increase in some age groups was balanced by the decrease in others. The latter reduction in predation mortality occurred when major predators of species with reducing size-at-age were decreasing in size themselves, or when cannibalism was an important source of juvenile mortality (in blue grenadier Macruronus novaezelandiae). We suggest that decreased size-at-age will be most detrimental to stock recovery when the main predators of the stock are not affected by the drivers causing changes in body size.