Three-dimensional (3D) photoluminescent crypto-images can be created by nanopatterning quantum dots (QDs) within a polymeric micro-object. A UV-sensitive photoresist, doped with (CdSe)ZnS core−shell QDs, is employed to fabricate fluorescent devices, by two-photon polymerization direct laser writing (TPP-DLW). In this work, we report on the expulsion of the majority of QDs from the irradiated area, caused by the crosslinking of the monomers, determining their accumulation on the photopolymer surface. At the same time, QDs get excited and trigger a surrounding thermal polymerization, leading to a variation of the spatial resolution of the fabricated structures. By opportunely combining these physical phenomena, it is possible to control the local density of QDs with nanometric resolution and, as a consequence, to tune the local photoemission of the fabricated polymeric structure. A photopolymer doped with five different concentrations of (CdSe)ZnS core−shell QDs is analyzed and tested. We define the best conditions to create nanostructures containing only few QDs to be integrated in optical devices, as well as to create 3D photoluminescent micro crypto-images. By TPP-DLW and one-photon lithography, a 3D fluorescent design can be concealed inside a polymeric microstructure that is swiftly fabricated using a photoresist. An example of a 3D crypto-image is shown to illustrate the technique.