The possibility of tuning the chemical moieties and their density plays a fundamental role in targeting surface-confined molecular structures and their functionalities at macro and nanoscale levels. Such interfacial control is crucial for engineered coating formation and biorecognition purposes, where the type and density of ligands/receptors at the surface affect the overall binding affinities and the device performance. Together with the well-established self-assembled monolayers, a surface modification approach based on polyelectrolytes (PEs) has gained importance to provide desired characteristics at the substrate interface. This review presents the innovations of functional PEs, modified in a preceding synthetic step, and their wide applicability in functional (a)biotic substrates. Examples of 2D and 3D architectures made by modified PEs are reviewed in relation with the reactive groups grafted to the PE backbones. The main focus lies on the strategy to use modified PEs to form bioengineered coatings for orthogonally anchoring biological entities, manufacturing biocidal/antifouling films, and their combinations in functional biosensing applications.