Oppositely charged polyelectrolyte multilayers (PEMs) were built up in a layer-by-layer (LbL) assembly on top of the conducting polymer channel of an organic electrochemical transistor (OECT), aiming to combine the advantages of well-established PEMs with a high performance electronic transducer. The multilayered film is a model system to investigate the impact of biofunctionalization on the operation of OECTs comprising a poly(3,4-ethylenedioxythiophene) polystyrenesulfonate (PEDOT:PSS) film as the electrically active layer. Understanding the mechanism of ion injection into the channel that is in direct contact with charged polymer films provides useful insights for novel biosensing applications such as nucleic acid sensing. Moreover, LbL is demonstrated to be a versatile electrode modification tool enabling tailored surface features in terms of thickness, softness, roughness, and charge. LbL assemblies built up on top of conducting polymers will aid the design of new bioelectronic platforms for drug delivery, tissue engineering, and medical diagnostics.