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Highly biocompatible multifunctional nanocomposites consisting of monodisperse manganese oxide nanoparticles with luminescent silica shells were synthesized by a combination of w/o-microemulsion techniques and common sol–gel procedures. The nanoparticles were characterized by TEM analysis, powder XRD, SQUID magnetometry, FT-IR, UV/vis and fluorescence spectroscopy and dynamic light scattering. Due to the presence of hydrophilic poly(ethylene glycol) (PEG) chains on the SiO2 surface, the nanocomposites are highly soluble and stable in various aqueous solutions, including physiological saline, buffer solutions and human blood serum. The average number of surface amino groups available for ligand binding on the particles was determined using a colorimetric assay with fluorescein isothiocyanate (FITC). This quantification is crucial for the drug loading capacity of the nanoparticles. SiO2 encapsulated MnO@SiO2 nanoparticles were less prone to Mn-leaching compared to nanoparticles coated with a conventional bi-functional dopamine–PEG ligand. The presence of a silica shell did not change the magnetic properties significantly, and therefore, the MnO@SiO2 nanocomposite particles showed a T1 contrast with relaxivity values comparable to those of PEGylated MnO nanoparticles. The cytotoxicity of the MnO@SiO2–PEG/NH2 nanoparticles was evaluated using primary cells of the innate immune system with bone marrow-derived polymorphonuclear neutrophils (BM-PMNs) as import phagocytes in the first line of defence against microbial pathogens, and bone marrow-derived dendritic cells (BMDCs), major regulators of the adaptive immunity. MnO@SiO2–PEG/NH2 nanoparticles have an acceptable toxicity profile and do not interact with BMDCs as shown by the lack of activation and uptake.