Benthic iron (Fe) fluxes from coastal sediments support phytoplankton blooms downstream of subpolar islands. We combine solid‐phase and pore‐water geochemical data, including its iron isotopic signature (δ56Feaq), to identify the main drivers of benthic Fe fluxes from sub‐Antarctic fjord and shelf sediments of South Georgia, and to evaluate the potential of δ56Feaq as a proxy for benthic Fe fluxes. A high accumulation rate of total organic carbon compresses the redox zonation in the near‐surface sediment column and controls benthic Fe efflux. Sites with low diffusive Fe fluxes show a broad δ56Feaq range close to the sediment‐water interface (−3.94 ± 0.14‰ to −0.98 ± 0.11‰), while sites with high benthic Fe fluxes exhibit a slightly narrower range (−3.14 ± 0.02‰ and −1.64 ± 0.06‰). The broader isotopic range in low benthic Fe flux settings reflects the diverse processes that entail low net benthic Fe fluxes into the bottom water. Low‐ and high rates of microbial iron reduction may result in similar Fe isotope composition of diffusive benthic Fe efflux, if the latter is combined with high rates of Fe removal from pore‐water by iron sulfide formation. A narrow range of δ56Feaq within the oxic redox zone appears to be a recurrent feature at sites of high benthic Fe fluxes, but we recommend accounting for all early diagenetic Fe cycling processes and the depositional regime when interpreting low δ56Feaq values in the near bottom water.