Southern elephant seals (Mirounga leonina) are known to move and aggregate while moulting, but little is known about their behaviour on land during this time. In this study, 60 adult females were monitored (23 with GPS tags) during four moulting seasons, between 2012 and 2016 at Kerguelen Archipelago, Indian Ocean. Population surveys were recorded each year (N = 230 daily counts) and habitat use was analysed in relation to the stage of the moult and local weather. Based on stage of moult, habitat use and movements on land, we classified the moult of elephant seals into three phases: 1) a “search phase” at the initial stage of moult when grass and wallow habitats were used and characterised by greater mean distances travelled on land per day compared with the two other phases, 2) a “resident phase”: during initial and mid-stage of moult when animals were found in grass and wallow habitats but with less distance moved on land, and 3) a “termination phase” at the final stage of moult where grass and beach habitats were occupied with no change in distances. Windchill and solar radiation influenced individual distances moved per day (mean 590 ± 237.0 m) at the mid and final stage of moult, such that animals travelled greater distances on days of low windchill or high solar radiation. Individual variation in distance moved and relative habitat use were also linked to body mass index (BMI) at arrival on the colony, as females with higher BMI moved less and preferred beach habitat. Moreover, the individual rate of moult increased with the use of wallows. Aggregation rate tended to be negatively correlated with distances moved. We therefore suggest that individuals face an energetic trade-off while moulting, balancing energy expenditure between movement and thermoregulation.