The effect of production method on the chemical and magnetic stability of a range of cobalt nanoparticles formed in polysiloxane copolymer micelles was studied. The nanoparticles were suspended in polydimethylsiloxane (PDMS) carrier fluids and are prototypes for use in biomedical applications. Three families of particles were investigated: cobalt particles in triblock copolymer micelles and silica-coated cobalt particles where the silica coating is formed either in toluene or PDMS carrier fluid. The silica coating effectively protects the cobalt particles from ongoing oxidation, with little change in the saturation magnetization of the particles observed over time and only a small shift in the centre of the field-cooled hysteresis loop observed. Temperature-dependent magnetization measurements show that the silica-coated particles have superparamagnetic blocking temperatures of 100–130 K compared with the non-silica-coated particles, which do not reach their characteristic blocking temperature below the melting point of the frozen fluids. This result is interpreted as a smaller magnetic core size in the silica-coated particles. The zero-field-cooled temperature-dependent magnetization of the silica-coated particles has two apparent superparamagnetic blocking temperatures, with a second, lower blocking temperature of approximately 15 K. This second apparent blocking temperature may be due to unreacted cobalt clusters in the suspensions or, alternatively, due to surface states on the nanoscale cobalt particles. The prototype silica-coated cobalt particles show promise for potential biomedical applications.