The area around the Antarctic Peninsula is projected to undergo rapid climatic changes affecting seasonal sea ice cover, water column stratification, terrestrial meltwater run-off, and related nutrient input and thus the conditions for primary production and organic carbon export. The impact of such environmental changes on benthic microbial communities is poorly understood. In this study, we investigated the impact of different sea ice cover and redox conditions on microbial community compositions from 7 different stations (330–450 m water depth) along a 400-mile transect from the eastern shelf of the Antarctic Peninsula to the west of the South Orkney Islands. Two deep stations (3000 m depth) were sampled for comparison. Samples were collected from 6 different intervals down to a depth of 16 cm. The diversity and composition of microbial communities were determined by 16S ribosomal RNA (rRNA) gene sequencing. Redox conditions in sediments with long ice-free periods showed that iron and sulfate reduction are dominant anaerobic pathways for carbon mineralization. In contrast, sediments at a heavily ice-covered station were dominated by the aerobic pathway, which accounted for >94 % of the total carbon degradation. Our results reveal that the microbial community composition at the station under heavy ice-cover differs significantly from stations under low ice-cover and tends to cluster separately, suggesting that sea ice cover is the main driver for changes in microbial community composition in the shelf sediments. Further, the frequency of marginal sea ice conditions (here defined as 5-35% sea ice cover) is significantly different between stations (p 0.001) and can explain 5 to 13% of the variation between microbial communities. The bacterial communities at stations under low ice-cover co-varied significantly with TOC content and porewater concentrations of ammonia, dissolved iron, and sulfide. This was reflected in the microbial community composition, where stations with low ice-cover were dominated by Desulfuromonadia, a taxon including many iron and sulfate reducers. At the station with heavy ice-cover, this class showed very low abundances. Our findings demonstrate that the benthic microbial composition and mediated-processes at various sites around the eastern Antarctic Peninsula are regulated by sea ice cover.