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Owing to changes in their chemistry and structure, polymers can be fabricated to demonstrate vastly different electrical conductivities over many orders of magnitude. At the high end of conductivity is the class of conducting polymers, which are ideal candidates for many applications in low-cost electronics. Here, we report the influence of the nature of the doping anion at high doping levels within the semi-metallic conducting polymer poly(3,4-ethylenedioxythiophene) (PEDOT) on its electronic transport properties. Hall effect measurements on a variety of PEDOT samples show that the choice of doping anion can lead to an order of magnitude enhancement in the charge carrier mobility > 3 cm2/Vs at conductivities approaching 3000 S/cm under ambient conditions. Grazing Incidence Wide Angle X-ray Scattering, Density Functional Theory calculations, and Molecular Dynamics simulations indicate that the chosen doping anion modifies the way PEDOT chains stack together. This link between structure and specific anion doping at high doping levels has ramifications for the fabrication of conducting polymer-based devices, The authors acknowledge the European Research Council (ERC-starting-grant 307596), the Swedish foundation for strategic research (project: “Nano-material and Scalable TE materials”), the Knut and Alice Wallenberg foundation (project “Power Paper” and “Tail of the Sun”), The Swedish Energy Agency (3833221), the Swedish Research Council via “Research Environment grant” on “Disposable paper fuel cells” (2016205990), and the Advanced Functional Materials Center at Linköping University. The authors thank Masatsugu Yamashita from the THz Sensing & Imaging Lab at RIKEN in Japan for conducting the THz reflectance spectroscopy experiments. D.R. Evans acknowledges the support of the Australian Research Council through the Future Fellowship scheme (FT160100300). J.W. Andreasen acknowledges the support of the European Research Council (ERC-consolidator-grant 681881). The computations were performed on resources provided by the Swedish National Infrastructure for Computing (SNIC) at NSC.