Although there is a wide range of legislative support for marine environmental policy and management, existing and emerging pressures continue to threaten biodiversity and ecosystems. Recent ambitious policies have represented a paradigm shift, moving from the traditional hands-off preservation towards more active forms of intervention through ecosystem restoration, with explicit targets for restoration of degraded ecosystems (2020/2030 EU Biodiversity Strategy). This work analyses the discourses and uncertainties in the cases of the fan mussel Pinna nobilis and the red coral Corallium rubrum in the Mediterranean, through a literature review and expert interviews. The major discourses are placed within a restoration framework based on the degree of intervention and the underlying motivations. The major discourse for both of these emblematic threatened species is ecocentric-based ‘Putting Nature First’, set around passive restoration (low-level intervention with protective measures to reduce stressor impact). Emerging discourses resulting from coastal developments and mass mortality events for the mussel and overfishing for corals, has required active restoration, with on-going small-scale actions. Both species highlight comparable shortcomings and constraints concerning restoration, particularly facing unknown baselines (what to restore to) and multiple uncertainties (population status, diseases, co-stressors, and long-term success of restoration). The top-down policy restoration targets lack detail towards implementation and most restoration efforts to-date are local-scale through bottom-up personal motivations, that have not been meeting policy targets. Lessons learned include the need to scale up passive measures and to couple with increased levels of active intervention with clear ideas on what, why, how and where to restore.