A novel, easy, two-step bottom-up fabrication strategy is introduced for the synthesis of 3D silver-silica hybrid nanostructures employing enzymatically generated silver nanoparticles (EGNPs) and plasma enhanced atomic layer deposition (PE-ALD). As ALD precursors tri-dimethyl-amino-silane (TDMAS) and oxygen plasma are used. Each precursor is individually exposed to the EGNPs to investigate the effect of TDMAS and oxygen plasma on the silver nanoparticles. It is observed that a metastable silver oxide surface is formed during the oxygen plasma step, which is proved by the selected area electron diffraction. The polycrystalline silver oxide decomposes right after the oxygen plasma dose step under the release of oxygen and lead to additional side-reactions with the TDMAS, which causes the observed hybrid structures. Various 3D silver-silica composite nanostructures, such as nanosponges and nanoflowers, are easily fabricated by tuning the PE-ALD parameters. The feature size increases up to 16 fold compared to the initial structures. The initial silver nanoparticles degrade to smaller silver substructures while applying PE-ALD. The particles size decreases with increasing the ALD cycle amount and lead to a further decrease of the side-reactions. Thus, the observed growth-effect seems to be limited by the amount of silver.