In this paper, the surface modification of CdSe- and CdZnS-based quantum dots (QDs) with a functional silica shell is reported. Functionalized silica shells are prepared by two routes: either by ligand exchange and a modified Stöber process or by a miniemulsion process with amphiphilic poly(oxyethylene) nonylphenylether also know as Igepal CO-520 (IG) as oligomeric amphiphile and modified silica precursors. The polymerizable groups on the functionalized silica shell allow covalent bonding to a polymer matrix and prevent demixing during polymerization and crosslinking. This allows the homogeneous incorporation of QDs in a crosslinked polymer matrix. This paper furthermore demonstrates that the resulting QDs, which are i) shielded with a proper silica shell and ii) functionalized with crosslinkable groups, can be used in two-photon-initiated polymerization processes in combination with different photoresists to obtain highly luminescent 3D structures. The resulting luminescent structures are attractive candidates for photonics and metamaterials research.