Metallic cobalt nanoparticles offer attractive magnetic properties but are vulnerable to oxidation, which suppresses their magnetization. In this article, we report the use of ion beam synthesis to produce ultra-small, oxidation-resistant, cobalt nanoparticles embedded within substoichiometric TiO2-δ thin films. Using high fluence implantation of cobalt at 20–60 keV, the particles were assembled with an average size of 1.5 ± 1 nm. The geometry and structure of the nanoparticles were studied using scanning transmission electron microscopy. Near-edge X-ray fluorescence spectroscopy on the L2,3 Co edges confirms that the majority of the particles beneath the surface are metallic, unoxidised cobalt. Further evidence of the metallic nature of the small particles is provided via their high magnetization and superparamagnetic response between 3 and 300 K with a low blocking temperature of 4.5 K. The magnetic properties were studied using a combination of vibrating sample magnetometry, element-resolved X-ray magnetic circular dichroism, and depth-resolved polarised neutron reflectometry. These techniques provide a unified picture of the magnetic metallic Co particles. We argue, based on these experimental observations and thermodynamic calculations, that the cobalt is protected against oxidation beneath the surface of titania owing to the enthalpic stability of TiO2 over CoO which inhibits solid state reactions.