Polymer core-shell nanocapsules with magnetic nanoparticles embedded in their oil cores were fabricated and applied as nano(photo)reactors. Superparamagnetic iron oxide nanoparticles (SPIONs) coated with oleic acid were first synthesized and characterized structurally, and their magnetic properties were determined. The capsules with chitosan-based shells were then formed in a one-step process by sonication-assisted mixing of (1) an aqueous solution of the hydrophobically derived chitosan and (2) oleic acid containing the dispersed SPIONs. In this way, magnetic capsules with a diameter of approximately 500-600 nm containing encapsulated SPIONs with an average diameter of approximately 20-30 nm were formed as revealed by dynamic light scattering and scanning transmission electron microscopy measurements. The composition and magnetic properties of the formed capsules were also followed using dynamic light scattering, electron microscopies, and magnetic force microscopy. The water-dispersible capsules, thanks to their magnetic properties, were then navigated in a static magnetic field gradient and transferred between the water and oil phases, as evidenced by fluorescence microscopy. In this way, the capsules could be loaded in a controlled way with a hydrophobic reactant, perylene, which was later photooxidized upon transferring the capsules to the aqueous phase. The capsules were shown to serve as robust reloadable nanoreactors/nanocontainers that via magnetic navigation can be transferred between immiscible phases without disruption. These features make them promising reusable systems not only for loading and carrying lipophilic actives, conducting useful reactions in the confined environment of the capsules, but also for magnetically separating and guiding the encapsulated active molecules to the site of action.