Implantable flexible neural interfaces (IfNIs) are capable of directly modulating signals of the central and peripheral nervous system by stimulating or recording the action potential. Despite outstanding results in acute experiments on animals and humans, their long-term biocompatibility is hampered by the effects of foreign body reactions that worsen electrical performance and cause tissue damage. We report on the fabrication of a polysaccharide nanostructured thin film as a coating of polyimide (PI)-based IfNIs. The layer-by-layer technique was used to coat the PI surface due to its versatility and ease of manufacturing. Two different LbL deposition techniques were tested and compared: dip coating and spin coating. Morphological and physiochemical characterization showed the presence of a very smooth and nanostructured thin film coating on the PI surface that remarkably enhanced surface hydrophilicity with respect to the bare PI surface for both the deposition techniques. However, spin coating offered more control over the fabrication properties, with the possibility to tune the coating’s physiochemical and morphological properties. Overall, the proposed coating strategies allowed the deposition of a biocompatible nanostructured film onto the PI surface and could represent a valid tool to enhance long-term IfNI biocompatibility by improving tissue/electrode integration.