Observational data show that climate in the Southern Ocean region is rapidly changing. However, past the instrumental period, our understanding of climate variability in the region is limited by a scarcity of high‐resolution palaeoclimate records. Alpine glaciers, present on many Southern Ocean islands, may provide such data because changes in their mass balance, extent and erosion rates often mark a response to climate shifts. Rock flour, the fine‐grained fraction of the glacial erosion process, is suspended in meltwater streams and transferred into the sediments of downstream lakes, continuously recording glacier variations. Here, we utilize this relationship to present a reconstruction of the Late Holocene glacier history of subantarctic South Georgia, using sediments from the glacier‐fed Middle Hamberg Lake. To fingerprint a glacial erosion/size signal, we used titanium counts, validated against changes in sediment density and grain size, allowing a continuous reconstruction of glacier variations over the past ∼1250 years. Together with local moraine evidence and supporting evidence from other Southern Hemisphere glaciers on New Zealand and in Patagonia, our findings reveal a series of consecutively diminishing Late Holocene advances. In addition to a glacier maximum before 1250 cal a BP, these include a two‐stage Litle Ice Age with advances around 300 and 120 cal a BP, in line with evidence from southern Patagonia. In addition, we present evidence for an unreported retreat behind present limits around 500 cal BP. Copyright © 2017 John Wiley & Sons, Ltd.