At variance with ferredoxins, Rieske-type proteins contain a chemically asymmetric iron–sulfur cluster. Nevertheless, X-ray crystallography apparently finds their [2Fe–2S] cores to be structurally symmetric or very close to symmetric (i.e. the four iron–sulfur bonds in the [2Fe– 2S] core are equidistant). Using a combination of advanced density-based approaches, including finite-temperature molecular dynamics to access thermal fluctuations and free-energy profiles, in conjunction with correlated wave- function-based methods we clearly predict an asymmetric core structure. This reveals a fundamental and intrinsic difference within the iron–sulfur clusters hosted by Rieske proteins and ferredoxins and thus opens up a new dimension for the ongoing efforts in understanding the role of Rieske-type [2Fe–2S] cluster in electron transfer processes that occur in almost all biological systems.