AbstractGlaciomarine fjords dominate the coastal margin of the West Antarctic Peninsula. Studies in similar habitats in the Arctic have shown that benthic biodiversity and ecosystem functioning in inner and middle fjord basins are reduced by turbidity and sedimentation disturbance caused by climate warming–enhanced glacial melting. In contrast, the inner and middle fjord basins along the West Antarctic Peninsula are characterized as productivity and biodiversity hotspots, but benthic ecosystem functions remain unevaluated. In 2015–2016, we conducted sediment respiration and 13C pulse‐chase experiments to assess benthic ecosystem functions along a five‐station transect at ~ 500–600 m depths from the inner Andvord Bay fjord, through to Gerlache Strait, and onto the open continental shelf. Incubation samples from the inner and middle basins of Andvord Bay showed peaks in background seafloor respiration, benthic biomass, and uptake of labeled algal biomass compared to more outlying stations; the continental shelf exhibited the lowest levels of these variables, as well as dissolved inorganic carbon production. Macrofaunal community uptake was responsible for most of the C processing in the inner and middle parts of the fjord (> 45%) while dissolved inorganic carbon was the dominant repository of processed C near the fjord mouth and on the continental shelf (> 80%). The inner parts of Andvord Bay are hotspots of benthic C‐cycling and metabolism, in addition to biodiversity. Ongoing climate warming is likely to negatively impact these inner‐fjord hotspots by increasing meltwater input and sedimentation disturbance, yielding a reduction in the input and recycling of labile detritus at the seafloor in the inner‐middle fjord.