Marine ecosystems, biodiversity, and fisheries are under strain worldwide due to global changes including climate warming and demographic pressure. To address this issue, many scientists and stakeholders advocate the use of an ecosystem approach for fisheries that integrates the numerous ecological and economic complexities at play rather than focusing on the management of individual target species. However, the operationalization of such an ecosystem approach remains challenging, especially from a bio-economic standpoint. Here, to address this issue, we propose a model of intermediate complexity (MICE) relying on multi-species, multi-fleet, and resource-based dynamics. Climate change effects are incorporated through an envelope model for the biological growth of fish species as a function of sea surface temperature. The model is calibrated for the small-scale fishery in French Guiana using a time series of fish landings and fishing effort from 2006 to 2018. From the calibrated model, a predictive fishing effort projection and RCP climate scenarios derived from IPCC, we explore the ecosystem dynamics and the fishery production at the horizon 2100. Our results demonstrate the long-term detrimental impact of both climate change and ecological competition on fish biodiversity. The prognosis is particularly catastrophic under the most pessimistic climate scenario, with a potential collapse of both biomass targeted species and fishing activity by 2100.