Obtaining small (< 50 nm), monodispersed, well-separated, single iron oxide core-silica (SiO2) shell nanoparticles for biomedical applications is still a challenge. Preferably, they are synthesised by inverse microemulsion method. However, substantial amount of aggregated and multicore core-shell nanoparticles is the undesired outcome of the method. In this study, we report on the production of less than 50 nm overall size, monodispersed, free of necking, single core iron oxide-SiO2 shell nanoparticles with tuneable shell thickness by a carefully optimized inverse microemulsion method. The high degree of control over the process is achieved by understanding the mechanism of core-shell nanoparticles formation. By varying the reaction time and precursor concentration, the thickness of silica layer on the core nanoparticles can be finely adjusted from 5 to 13 nm. Residual reactions during the workup were inhibited by a combination of pH control with shock freezing and ultracentrifuging. These high-quality tuneable core-shell nanocomposite particles exhibit superparamagnetic character and sufficiently high magnetization with great potential for biomedical applications (e.g. MRI, cell separation and magnetically driven drug delivery systems) either as-prepared or by additional surface modification for improved biocompatibility.