Seagrass and macroalgae beds are key blue carbon ecosystems in the ocean. However, coastal development and climate change are sparking a growing concern about the vulnerability of sediment organic carbon (OC) to remineralization after macrophyte perturbation. Thus, the aim of this study was to assess the potential of long-term remineralization of sediment OC stocks (1 year) in coastal vegetated habitats (i.e., seagrasses Zostera noltei and Cymodocea nodosa, macroalgae Caulerpa prolifera and unvegetated sediment) after complete disturbance of macrophyte meadows under conducive conditions to microorganisms growth (i.e., oxygen saturated, non-nutrient limitation, turbulence and dark). Leached dissolved organic carbon (DOC) from particulate organic carbon (POC) remineralization, carbonate dissolution and photo-reactivity of long-term persistent DOC were also evaluated. Our results evidenced that, sediment OC from Z. noltei and unvegetated habitats were entirely remineralized to CO2. However, sediment OC from C. nodosa and C. prolifera communities exhibited a significant fraction of recalcitrant OC, and therefore, a 42 and 46% of the sediment OC still remained after 1 year of culture, respectively. POC remineralization released relevant amounts of both labile and recalcitrant DOC, which showed low photo-reactivity. Finally, we discuss that the main argument to promote management, monitoring, and restoration programs for macrophytes is usually based on their sediment OC deposit, which favor larger species. The study presented here adds arguments to also include small macrophyte species, since their sediment OC may be highly labile and entirely remineralized to CO2 once these habitats are disturbed.