The incorporation of gold nanoparticles in biodegradable polymeric nanostructures with controlled shape and size is of interest toward different applications in nanomedicine. Properties of the polymer such as drug loading and antibody functionalization can be combined with the plasmonic properties of gold nanoparticles, to yield advanced hybrid materials. This study presents a new way to synthesize multicompartmental microgels, fibers, or cylinders, with embedded anisotropic gold nanoparticles. Gold nanoparticles dispersed in an organic solvent can be embedded within the poly(lactic-co-glycolic acid) (PLGA) matrix of polymeric microstructures, when prepared via electrohydrodynamic co-jetting. Prior functionalization of the plasmonic nanoparticles with Raman active molecules allows for imaging of the nanocomposites by surface-enhanced Raman scattering (SERS) microscopy, thereby revealing nanoparticle distribution and photostability. These exceptionally stable hybrid materials, when used in combination with 3D SERS microscopy, offer new opportunities for bioimaging, in particular when long-term monitoring is required.