In order to assist fisheries managers, ecological indicators are needed to evaluate the effects of fishing activities on marine ecosystems and to improve communication of these effects in both public and scientific contexts. Finding appropriate indicators is challenging given the complexity of marine food webs as well as the ecosystem response to fishing pressure. In this study, an end-to-end model developed in the Gulf of Gabes ecosystem (Tunisia) was used to compare the performance of a set of ecosystem indicators in assessing the impact of fishing. This end-to-end model aimed to represent the ecosystem functioning by coupling two existing sub-models, the multispecies individual-based model OSMOSE, representing the dynamics of exploited species and the biogeochemical model Eco3M-Med. The aim of the indicator selection method is to evaluate the sensitivity of a set of ecological indicators regardless the fishing management plan. This method was performed in two major steps. The first step consisted in simulating three simple contrasted fishing strategies in the OSMOSE model exploiting target species (i.e. high trophic level, low trophic level or all species) and then applying a fishing effort multiplier for each fishing strategy to the focus target species. In the second step, three paradigms defining the desirable properties of an ecological indicator have been specified: i/the indicator decreases with increasing fishing pressure, ii/the indicator responds linearly to an increase in fishing pressure and iii/the indicator responds consistently across different fishing strategies. Our results highlighted that the majority of indicators have quite similar performance regarding the trend and the linearity of their responses. However, the size-based indicators seem to be the most robust to track ecosystem effects of fishing when the fishing strategy changes. A focus on size-based indicators showed that Large Fish Indicators (40 cm) derived from demersal or all surveyed species were the most suitable to reflect a change in the status of the Gulf of Gabes ecosystem due to fishing pressure.