Research and practical experience have shown that partial replacement of cement by metakaolin improves concrete durability as a result of the refinement of the pore structure. While much research has been presented on concrete performance with metakaolin, it is scarce concerning the transport properties of chlorides in concrete with metakaolin, in natural conditions (i.e., un-accelerated). This study determines the chloride diffusion coefficients for several concretes with vary levels of cement replacement with metakaolin, and compares these results with chloride migration coefficients obtained from accelerated laboratory testing. In this study, two cement types (CEM I 42,5R and CEM IV/A 42,5) and two cement contents levels where used with metakaolin replacement levels varying from 10-20%. Concretes where tested for fresh properties, compressive strength, electrical resistivity, chloride ingress characteristics (natural diffusion and migration), and mercury intrusion porosimetry. The results show improved strength, durability properties and chloride penetration resistance of concretes with metakaolin. Furthermore, the use of metakaolin in fly ash concrete improves the early age performance of the concrete (<90 days), counteracting the delay in strength and durability gain typically associated with fly ash concrete. The results obtained from this study fulfil the lack of critical input for service life design models of reinforced concrete structures in chloride environments, with emphasis on concretes with metakaolin replacement.