You can synthesize nanoparticles by reducing some ions with green synthesis. Then separate them, wash them, disperse them in an aqueous solution of another precursor, and reduce another metal layer on the surface of the nanoparticles with green synthesis. You will get core/shell nanoparticles.
Article 'Green' synthesis of metals and their oxide nanoparticles: A...
From current synthesis methods, one approach to make them "greener" would be to change reactants and/or solvents to non-toxic, more environmental-bening or affordable compounds.
Yes, green synthesis methods can be adapted for complex nanostructures such as core-shell, Janus, and multi-metallic nanoparticles, though there are some unique challenges and considerations compared to simpler nanoparticle systems.