In the Southern Ocean, iron plays a key role in limiting biological production. Studies of the iron supply to the surface mixed layer have traditionally focused on the aeolian and sediment contributions, but recent work has highlighted the importance of the vertical supply from below. We have performed a model study in which the biogeochemical model REcoM2 was coupled to two different ocean models, the Finite Element Sea-ice Ocean Model (FESOM) and the MIT general circulation model (MITgcm) and analyzed the magnitude of the iron sources from below in the two models. Our results revealed a remarkable difference in terms of mode and magnitude of transport; the mean iron supply from below in the Southern Ocean was on average four times higher in MITgcm than in FESOM. The dominant pathway was entrainment in MITgcm, whereas diffusion dominated in FESOM. We discuss how the difference in the depth and seasonal amplitude of the mixed layer between the models has a major effect on the vertical iron profile and thereby also on the iron fluxes. A further effect of the difference in supply is that the fraction of exported net primary production is higher in MITgcm than in FESOM, showing that the choice of ocean model has a significant impact on the modeled carbon cycle in the Southern Ocean, with possible implications for model runs predicting the future carbon uptake in the region.