Mussel-inspired polydopamine (PDA) initiates a multifunctional modification route that leads to the generation of novel advanced materials and their applications. However, existing PDA deposition techniques still exhibit poor spatial control, have a very limited capability of micropatterning, and do not allow local tuning of the PDA topography. Herein, PDA deposition based on multiphoton lithography (MPL) is demonstrated, which enables full spatial and temporal control with nearly total freedom of patterning design. Using MPL, 2D microstructures of complex design are achieved with pattern precision of 0.8 µm without the need of a photomask or stamp. Moreover, this approach permits adjusting the morphology and thickness of the fabricated microstructure within one deposition step, resulting in a unique tunability of material properties. The chemical composition of PDA is confirmed and its ability for protein enzyme immobilization is demonstrated. This work presents a new methodology for high-precision and complete control of PDA deposition, enabling PDA incorporation in applications where fine and precise local surface functionalization is required. Possible applications include multicomponent functional elements and devices in microfluidics or lab-on-a-chip systems. © 2022 The Authors