Spatial and seasonal dynamics of microbial loop fluxes were investigated in contrasting productivity regimes in the Indian sector of the Southern Ocean. Observations carried out in late summer (February–March 2018; project MOBYDICK) revealed higher microbial biomasses and fluxes in the naturally iron‐fertilized surface waters of Kerguelen island in comparison to surrounding off‐plateau waters. Differences were most pronounced for bacterial heterotrophic production (2.3‐fold), the abundance of heterotrophic nanoflagellates (HNF; 2.7‐fold). Independent of site, grazing by HNF was the main loss process of bacterial production (80–100%), while virus‐induced mortality was low (< 9%). Combining these results with observations from previous investigations during early spring and summer allowed us to describe seasonal patterns in microbial food web fluxes and to compare these to carbon export in the iron‐fertilized and high‐nutrient, low‐chlorophyll (HNLC) Southern Ocean. Our data suggest an overall less efficient microbial food web during spring and summer, when respiration and viral lysis, respectively, represent important loss terms of bacterially‐mediated carbon. In late summer, primary production is more efficiently transferred to bacterial biomass and HNF and thus available for higher trophic levels. These results provide a new insight into the seasonal variability and the quantitative importance of microbial food web processes for the fate of primary production in the Southern Ocean