Poly(3,4-ethylenedioxythiophene) (PEDOT) was polymerized with the biological dopants dextran sulphate and chondroitin sulphate. Polymer physical and mechanical properties were investigated using quartz crystal microgravimetry with dissipation monitoring and atomic force microscopy, revealing polymer shear modulus and interfacial roughness to be significantly altered as a function of the dopant species. The adsorption of fibronectin, an important extracellular protein that is critical for a range of cellular functions and processes, was investigated using QCM-D, revealing protein adsorption to be increased on the DS doped PEDOT film relative to the CS doped film. PEDOT films have traditionally been doped with synthetic counterions such as polystyrene sulphonate (PSS), however the incorporation of biological molecules as the counterion, which has been shown to improve polymer biofunctionality, has received far less attention. In particular, there has been little detailed study on the impact of incorporating polyelectrolyte biomolecules into the PEDOT polymer matrix on fundamental polymer properties which are critical for biomedical applications. This investigation provides a detailed characterization of the interfacial and mechanical properties of biologically doped PEDOT films, as well as the efficacy of the composite films to bind and retain extracellular proteins of the type that are critical to the biocompatibility of the polymeric material.