A novel method for functionalising solution based polyaniline (PAni) nanofibres is reported whereby the degree of side-chain attachment can be controllably altered. The covalent attachment of functional side-groups to the surface of PAni nanostructures is achieved by post-polymerisation reflux in the presence of a nucleophile and the functionalised nanomaterial can be purified by simple centrifugation. The technique is therefore easily scalable. We demonstrate that control over the extent of side-chain attachment can be achieved simply by altering the amount of nucleophile added during reflux. We provide evidence that covalently attached carboxlate side-chains influence the doping mechanism of polyaniline and can be used to introduce self-doping behaviour. Acid functionalised nanofibres remain redox active and retain their optical switching capabilities in response to changes in the local chemical environment, thus making them suitable for adaptive sensing applications.