Understanding the interplay between the nanomechanical properties of organic electronic materials and their electronic properties is central to developing sensors and transducers for applications ranging from immunosensing to e-skin. Controlling organic device operations in aqueous electrolyte solutions and their mechanical compliance with the host tissue or living systems, as for instance in active implants for the recording or stimulation of neural signals, is still largely unexplored. Here, we implemented bimodal AFM to map the nanomechanical and structural properties of thin films made from poly(3,4-ethylenedioxythiophene):poly(styrene-sulfonate) (PEDOT:PSS), the most widely used conducting polymer blend, during operation as a microelectrode in an electrolyte solution. Nanomechanical maps showed the film consisting of a granular structure made from PEDOT:PSS regions embedded in the PSS matrix. The film swelled upon immersion in an aqueous solution. In operando bimodal AFM data obtained by applying a sequence of doping/de-doping bias cycles showed a significant decrease in the modulus (70%) that saturated after about 10 cycles. A similar sequence of biases at the opposite polarity did not significantly influence the mechanical behaviour of PEDOT:PSS. The decrease in the modulus was explained by the development of persistent hydration, which was enhanced by the cations trapped inside the organic electronic material.