Salt marshes are among the most efficient blue carbon sinks worldwide. The fate of this carbon is uncertain due to limited knowledge about organic matter (OM) decomposition processes under sea-level rise. In an in-situ manipulative experiment, we compared salt marsh OM decomposition and quality across simulated sea-level scenarios (by modifying the inundation) and litter types (absorptive root, fine transportive root, leaves, and rhizomes of Halimione portulacoide) for 170 days. The litter decomposition varied only between the inundation treatments with the longest and shortest durations, while the decomposition differed significantly across litter types, with absorptive roots releasing up to 40% less carbon than other litters. Changes in lignin composition were minimal for absorptive roots and were unaffected by sea-level rise scenarios. Our study suggests that (i) current projections of sea-level rise are unlikely to decrease litter decomposition; (ii) separating litter types might lead to better assessments of salt marshes’ OM dynamics.