Conducting polyaniline protonated with sulphonic flexible counter-ions was investigated by quasielastic incoherent neutron scattering. In addition to their role in electrical properties, the flexible counter-ions also increase the elasticity of the samples. As in the case of more rigid counter-ions, polymer chains appear as very stiff objects whose dynamics is completely outside the investigated time scale. Conversely, the counter-ion dynamics was proved to be of major importance in charge transport since a dynamical transition is observed precisely in the temperature range where the electronic properties change from a metallic to a semiconducting regime.