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Semiconductor quantum dots (QDs) are widely used for optical applications and bioimaging. In comparison to organic dyes used for fluorescent labeling, QDs exhibit very high photostability and can be further surface modified. Equipping QDs with magnetic properties (mQDs) makes it possible to combine fluorescence and magnetic resonance imaging analyses. For this purpose, we have prepared water-dispersible and magnetic CdTe/ZnS mQDs, whereby ferrous ions are selectively incorporated in either their cores or their shells. This study aims at understanding the differences in optical, structural, and magnetic properties between these core- and shell-doped mQDs. Field-dependent isothermal magnetic susceptibility measurements show that shell-doped mQDs exhibit paramagnetic and their core-doped equivalents superparamagnetic behavior near room temperature. Shell doping results in about 1.7 times higher photoluminescence quantum yields and 1.4 times higher doping efficiency than core doping. X-ray diffraction patterns reveal that core doping leads to defects in the lattice and hence to a severe decrease in crystallinity, whereas shell doping has no significant impact on the crystal structure and consequently fewer disadvantages regarding the mQD’s quantum yield. These selective doping approaches, particularly shell doping, allow for the tailored design of paramagnetic QDs having modifiable and biocompatible particle surfaces. The organic ligands—in this study N-acetyl-l-cysteine—sufficiently prevent leakage of toxic metal ions, as shown by cytotoxicity assays with HepG2 cells. Confocal laser scanning microscopy shows that mQDs are internalized by these cells and accumulated near their nuclei. This study shows that biocompatible, fluorescent, and paramagnetic QDs are promising photostable labels for multimodal bioimaging.