We used Ecopath with Ecosim to describe the structure and functioning of the shelf ecosystem of the island of Cyprus (eastern Mediterranean) and simulate a series of scenarios related to fisheries and ecosystem management strategies. Analysis was based on a previous 2015–17 model of the same ecosystem, updated with recent data on recreational catches and diets. Two new models were built based on that model, one for 2005 and one for 2021, which along with time series of effort, biomass and catches were used to fit model predictions to observations and simulate the evolution of the ecosystem in the next 30 years, under different fishing scenarios. A total of 32 scenarios were tested related to either changes in fishing effort by fishing fleet, or changes in fishing mortality of selected predatory and invasive groups, along with the business as usual scenario. Ecosystem responses were expressed through a series of ecological and fisheries-related indicators. A 25% increase or decrease in overall fishing mortality, especially coming from recreational fisheries, was predicted to have a dramatic impact on the biomass (and consequently catch) of large pelagic fishes, which seemed to act as regulators in the ecosystem impacting most groups directly or indirectly via trophic interactions and competition. Instead, large demersal fishes were predicted to respond differently to such fishing changes, with less intense biomass fluctuations and a tendency to quickly return to the initial state. Invasive lionfish and pufferfishes were also greatly affected by targeted increased fishing mortalities but seemed to be able to return to initial biomasses in only a few years when mortalities went back to normal. Predatory biomass and catch, total catch, native species catch and catch value, all increased in scenarios with reduced fishing mortality and decreased in the opposite case. Kempton’s Q diversity index decreased in most scenarios, however, most key ecosystem indicators like the total system throughput (TST), Finn's cycling index (FCI) and mean path length (PL), as well as mean transfer efficiency (TE) remained more or less constant in all simulations, indicating an ecosystem stability in terms of its fundamental traits, such as its ecological size (i.e., the sum of flows), trophic complexity and maturity. Simulations revealed the magnitude of uncertainties that ecosystem’s complexity can introduce to fisheries management and highlighted the importance of holistic scientific advice for managers.