This work presents a highly effective approach for the chemical purification of directly written 2D and 3D gold nanostructures suitable for plasmonics, biomolecule immobilisation, and nanoelectronics. Gold nano- and microstructures can be fabricated by one-step direct-write lithography process using focused electron beam induced deposition (FEBID). Typically, as-deposited gold nanostructures suffer from a low Au content and unacceptably high carbon contamination. We show that the undesirable carbon contamination can be diminished using a two-step process – a combination of optimized deposition followed by appropriate postdeposition cleaning. Starting from the common metal-organic precursor Me2-Au-tfac, it is demonstrated that the Au content in pristine FEBID nanostructures can be increased from 30 atom % to as much as 72 atom %, depending on the sustained electron beam dose. As a second step, oxygen-plasma treatment is established to further enhance the Au content in the structures, while preserving their morphology to a high degree. This two-step process represents a simple, feasible and high-throughput method for direct writing of purer gold nanostructures that can enable their future use for demanding applications.