In recent years, the use of organic materials to infer conductivity in biomedical devices has received increasing attention. Typical inorganic semiconductors and conductors are rigid and expensive, usually require multiple processing steps and are unsuitable for biomedical applications. Electrochemically or chemically doped conjugated polymers help to overcome these problems due to their stability, low cost, light weight and excellent electrical and optical properties. The conducting polymer poly(3,4-ethylenedioxythiophene): polystyrene sulfonate (PEDOT:PSS) is the material of choice for biomedical applications as it is water soluble, however, there are growing concerns around its stabilizer, PSS, due to its release of acidic products upon degradation in-vivo. Here, we report the successful synthesis of PEDOT nanoparticles using hyaluronic acid (HA) as a stabilizer via an oxidative miniemulsion polymerisation technique. This improves the bioactivity and hydrophilicity of nanoparticles. The effect of varying amounts of HA and different molar ratios of EDOT:TOS has been studied and their role in the conductive and morphological properties of final nanoparticles has been fully elucidated. Furthermore, bioactivity and biocompatibility of the nanoparticles are demonstrated for customizable in vivo applications. Nanoparticles were found to have a conductivity up to 10 times greater than pristine PEDOT:PSS with increased addition of oxidant. The proposed easy-to-manufacture approach, along with the highlighted superior properties, expands the potential of conductive polymers in future customizable biological applications such as tissue scaffolds, nerve conduits and cardiac patches and represents a real breakthrough from the current state of the art.