Luminescence-encoded microbeads are important tools for many applications in the life and material sciences that utilize luminescence detection as well as multiplexing and barcoding strategies. The preparation of such beads often involves the staining of premanufactured beads with molecular luminophores using simple swelling procedures or surface functionalization with layer-by-layer (LbL) techniques. Alternatively, these luminophores are sterically incorporated during the polymerization reaction yielding the polymer beads. The favorable optical properties of semiconductor quantum dots (QDs), which present broadly excitable, size-tunable, narrow emission bands and low photobleaching sensitivity, triggered the preparation of beads stained with QDs. However, the colloidal nature and the surface chemistry of these QDs, which largely controls their luminescence properties, introduce new challenges to bead encoding that have been barely systematically assessed. To establish a straightforward approach for the bead encoding with QDs with minimized loss in luminescence, we systematically assessed the incorporation of oleic acid/oleylamine-stabilized CdSe/CdS-core/shell-QDs into 0.5–2.5 µm-sized polystyrene (PS) microspheres by a simple dispersion polymerization synthesis that was first optimized with the organic dye Nile Red. Parameters addressed for the preparation of luminophore-encoded beads include the use of a polymer-compatible ligand such as benzyldimethyloctadecylammonium chloride (OBDAC) for the QDs, and crosslinking to prevent luminophore leakage. The physico-chemical and optical properties of the resulting beads were investigated with electron microscopy, dynamic light scattering, optical spectroscopy, and fluorescence microscopy. Particle size distribution, fluorescence quantum yield of the encapsulated QDs, and QD leaking stability were used as measures for bead quality. The derived optimized bead encoding procedure enables the reproducible preparation of bright PS microbeads encoded with organic dyes as well as with CdSe/CdS-QDs. Although these beads show a reduced photoluminescence quantum yield compared to the initially very strongly luminescent QDs, with values of about 35%, their photoluminescence quantum yield is nevertheless still moderate.