Magnetic nanoparticles (MnPs) are relevant to a wide range of applications including high density information storage and magnetic resonance imaging to name but a few. Among the materials available to prepare MnPs, FePt is attracting growing attention. However, to harvest the strongest magnetic properties of FePt MnPs, a thermal annealing is often required to convert face-centered cubic as synthesized nPs into its tetragonal phase. Rarely addressed are the potential side effects of such treatments on the magnetic properties. In this study, we focus on the impact of silica shells often used in strategies aiming at overcoming MnP coalescence during the thermal annealing. While we show that this shell does prevent sintering, and that fcc-to-fct conversion does occur, we also reveal the formation of silicide, which can prevent the stronger magnetic properties of fct-FePt MnPs from being fully realised. This report therefore sheds lights on poorly investigated and understood interfacial phenomena occurring during the thermal annealing of MnPs and, by doing so, also highlights the benefits of developing new strategies to avoid silicide formation.