The Southern Ocean remains one of the least explored marine environments. The investigation of temporal microbial dynamics has thus far been hampered by the limited access to this remote ocean. We present here high‐resolution seasonal observations of the prokaryotic community composition during phytoplankton blooms induced by natural iron fertilization. A total of 18 seawater samples was collected by a moored remote autonomous sampler over 4 months at 5‐11 day intervals in offshore surface waters (central Kerguelen Plateau). Illumina sequencing of the 16S rRNA gene revealed that among the most abundant ASVs, SAR92 and Aurantivirga were the first bloom responders, Pseudomonadaceae, Nitrincolaceae, and Polaribacter had successive peaks during the spring bloom decline, and Amylibacter increased in relative abundance later in the season. SAR11 and SUP05 were abundant prior to and after the blooms. Using network analysis, we identified two groups of diatoms representative of the spring and summer bloom that had opposite correlation patterns with prokaryotic taxa. Our study provides the first seasonal picture of microbial community dynamics in the open Southern Ocean and thereby offers biological insights to the cycling of carbon and iron, and to an important puzzling issue that is the modest nitrate decrease associated to iron fertilization.