Microplankton community structure and particulate matter stoichiometry were investigated in a late summer survey across the Subantarctic and Polar Front in the Indian sector of the Southern Ocean. Microplankton community structure exerted a first order control on PON:POP stoichiometry with diatom-dominated samples exhibiting much lower ratios (4–6) than dinoflagellate and ciliate-dominated samples (10–21). A significant fraction of the total chlorophyll a (30–70%) was located beneath the euphotic zone and mixed layer and sub-surface chlorophyll features were associated to transition layers. Although microplankton community structure and biomass was similar between mixed and transition layers, the latter was characterized by elevated Chl:POC ratios indicating photoacclimation of mixed layer communities. Empty diatom frustules, in particular of Fragilariopsis kerguelensis and Pseudo-nitzschia, were found to accumulate in the Antarctic Zone transition layer and were associated to elevated BSi:POC ratios. Furthermore, high Si(OH)4 diffusive fluxes (>1 mmol m2 d−1) into the transition layer appeared likely to sustain silicification. We suggest transition layers as key areas of C and Si decoupling through (1) physiological constraints on carbon and silicon fixation (2) as active foraging sites for grazers that preferentially remineralize carbon. On the Kerguelen Plateau, the dominant contribution of Chaetoceros Hyalochaete resting spores to microplankton biomass resulted in a three-fold enhancement of POC concentration at 250 m, compared to other stations. These findings further highlight the importance of diatom resting spores as a significant vector of carbon export through the intense remineralization horizons characteristing Southern Ocean ecosystems.