The introduction of ecosystem-based management measures for Baltic fisheries to achieve Good Environmental Status (GES) within the MSFD (Marine Strategy Framework Directive) and the HELCOM (Baltic Marine Environment Protection Commission) requires tools that can evaluate measures to reduce the spatial footprint on the seabed. We applied the DISPLACE modelling platform at the wide-scale Baltic Sea to evaluate the effect of different spatial fishery management measures such as area closures, both in terms of impact on benthic habitats and impacts on catch, revenue and profit for international fisheries. DISPLACE simulates individual fishing vessels (>12 m length using bottom-contact gears) and how they redistribute their fishing effort given spatial or temporal closures. A new module, informed from available science for projecting benthos dynamics in response to fishing pressure, provides quantification of depletion from fishing and recovery of specific benthic habitats and seabed types. This study evaluates different scenarios and trade-offs with the objective to identify effective measures to achieve GES by 2021 as stipulated by the Baltic Sea Action Plan. A suite of time and space mitigation scenarios are defined to compare the effects of a gradient of fishing restrictions and closures in different areas, habitat types, jurisdictions, breaking down to the impact from different type of gears and on several fisheries economics. The results obtained are intended to help the EU maritime policy in finding ways to improve the management of the Baltic Sea seafloor along reducing the human footprint induced by the fishing activities, while considering biological and economic impacts.