Ice cores and offshore sedimentary records demonstrate enhanced ice loss along Antarctic coastal margins during millennial-scale warm intervals within the last glacial termination. However, the distal location and short temporal coverage of these records leads to uncertainty in both the spatial footprint of ice loss, and whether millennial-scale ice response occurs outside of glacial terminations. Here we present a >100kyr archive of periodic transitions in subglacial precipitate mineralogy that are synchronous with Late Pleistocene millennial-scale climate cycles. Geochemical and geochronologic data provide evidence for opal formation during cold periods via cryoconcentration of subglacial brine, and calcite formation during warm periods through the addition of subglacial meltwater originating from the ice sheet interior. These freeze-flush cycles represent cyclic changes in subglacial hydrologic-connectivity driven by ice sheet velocity fluctuations. Our findings imply that oscillating Southern Ocean temperatures drive a dynamic response in the Antarctic ice sheet on millennial timescales, regardless of the background climate state.