The continental shelf off central-south Chile sustains highly productive fisheries. The sustainability of these resources is nevertheless in jeopardy since many of them are either overexploited or collapsed. Using an allometrically (size-based) parameterized model of the shelf’s food web, we analyze the likely ecosystem effects of fishing in this system by measuring the response of several ecological indicators to changes in fishing pressure. Indicators performed as follows: (i) insensitive (community biomass stability, clustering coefficient), (ii) varying directly (number of species going "extinct") or inversely (NBSS coefficient of determination), and (iii) abrupt inverse change, but then insensitive beyond a threshold (FiB index, Mean Trophic Level of the Catch, NBSS slope, and total community biomass). The latter four indicators seem less informative for management once a fishery has developed. Simulations showed that fishing any single species affected several species through food web-mediated mechanisms, then making difficult to predict the effects of fishing on the abundance of target and non-target species. Therefore, conservation measures should not rely exclusively on reducing fishing mortality for a given target species, but also take into account the status of interacting species.The continental shelf off central-south Chile sustains highly productive fisheries. The sustainability of these resources is nevertheless in jeopardy since many of them are either overexploited or collapsed. Using an allometrically (size-based) parameterized model of the shelf’s food web, we analyze the likely ecosystem effects of fishing in this system by measuring the response of several ecological indicators to changes in fishing pressure. Indicators performed as follows: i) insensitive (community biomass stability, clustering coefficient), ii) varying directly (number of species going "extinct") or inversely (Normalized biomass size spectra (NBSS) coefficient of determination), and iii) abrupt inverse change, but then insensitive beyond a threshold (Fishing in Balance (FiB) index, Mean Trophic Level of the Catch, NBSS slope, and total community biomass). The latter four indicators seem less informative for management once a fishery has developed. Simulations showed that fishing any single species affected several species through food web-mediated mechanisms, then making difficult to predict the effects of fishing on the abundance of target and non-target species. Therefore, conservation measures should not rely exclusively on reducing fishing mortality for a given target species, but also take into account the status of interacting species.