ntarctic sea-ice extent, primary productivity and ocean circulation represent interconnected systems that form important components of the global carbon cycle. Subdecadal to centennial-scale variability can influence the characteristics and interactions of these systems, but observational records are too short to evaluate the impacts of this variability over longer timescales. Here, we use a 170-m-long sediment core collected from Integrated Ocean Drilling Program Site U1357B, offshore Adélie Land, East Antarctica to disentangle the impacts of sea ice and subdecadal climate variability on phytoplankton bloom frequency over the last ~11,400 years. We apply X-ray computed tomography, Ice Proxy for the Southern Ocean with 25 carbon atoms, diatom, physical property and geochemical analyses to the core, which contains an annually resolved, continuously laminated archive of phytoplankton bloom events. Bloom events occurred annually to biennially through most of the Holocene, but became less frequent (~2–7 years) at ~4.5 ka when coastal sea ice intensified. We propose that coastal sea-ice intensification subdued annual sea-ice break-out, causing an increased sensitivity of sea-ice dynamics to subdecadal climate modes, leading to a subdecadal frequency of bloom events. Our data suggest that projected loss of coastal sea ice will impact the influence of subdecadal variability on Antarctic margin primary productivity, altering food webs and carbon-cycling processes at seasonal timescales.