<p>The seabed is essential to the health of marine ecosystems, supporting key species and providing critical ecosystem services. However, human activities exert increasing pressures that degrade and reduce benthic habitats. Protecting sea floor integrity requires ecosystem-based management (EBM) capable of addressing impacts across sectors and national borders. Achieving this is supported by governance arrangements that coordinate actions among government bodies, countries, and administrative levels while aligning sectoral and environmental policies. To enhance seabed management, the EU has introduced threshold values that define acceptable limits of habitat loss and disturbance. In parallel, HELCOM has launched regional cooperation to develop a common approach among Baltic Sea countries to strengthen the protection of benthic habitats. This paper presents findings from a qualitative analysis of these two recent initiatives. The results indicate that the threshold values have the potential to improve the implementation of the EU Marine Strategy Framework Directive but show also potential limitations of the approach. Likewise, HELCOM’s joint approach may establish a new form of collaborative governance to support Baltic Sea seabed management, but some changes in HELCOM’s practices would allow the approach to reach its full potential. We conclude by outlining how these initiatives, if well-coordinated, can together reinforce governance approaches that address interactions within ecosystems and between ecosystems and society, promote long term adaptive management, and manage multiple spatial and administrative scales that are all key features of successful EBM.</p>