• Restricting fishing areas does not equate to reducing ecosystem impacts on benthic habitats.
• Displacing fishing efforts can offset the gains in partial habitat protection.
• The benthic status in Kattegat improves more than the benthic status in central Baltic when using spatial management measures.
• Largest improvement is achieved by protecting long-lived communities from high-impact fisheries.
• Healthy fish stocks reduce the risk to both the seafloor integrity and fishery economics.