Diatoms are the main primary producers in the Southern Ocean, governing the major nutrient cycles. Fragilariopsis kerguelensis (O’Meara) Hust. is the most abundant diatom species in the Southern Ocean and its paleo-oceanographic record is frequently used to reconstruct the past position and nutrient characteristics of the Antarctic polar front. Here we report on the responses of F. kerguelensis on prolonged exposure to a range of iron concentrations, allowing a characterization of morphological and nutrient-depletion changes in relation to iron status. Under iron limitation, F. kerguelensis grew slower, cells became smaller, chains became shorter, and the nutrient-depletion ratios changed. Prolonged exposure to iron limitation caused F. kerguelensis to decrease its surface area and volume 2-fold, and to increase its surface-to-volume ratio by 25%. With the decrease in growth rates, silicon (Si) and phosphorus (P) depletion per cell remained fairly constant, but when normalized per surface area (Si) or per cell volume (P), depletion increased. In contrast, nitrogen (N) depletion per cell decreased significantly together with the decrease in growth rates but was constant when normalized per cell volume. The different response in Si, P, and N depletion resulted in changes in the nutrient-depletion ratios, most notably in the Si:N ratio, which significantly increased, and in the N:P ratio, which significantly decreased with decreasing growth rates. It is concluded that under iron limitation, variation in cell size and/or nutrient depletion ultimately can cause changes in oceanic biogeochemical nutrient cycles. It enables the use of cell size of F. kerguelensis as a paleo-oceanographic proxy.