An in situ approach for the synthesis of Fe₃O₄ nanoparticles combined with a SiO₂ coating process was employed to prepare Fe₃O₄@GNF@SiO>₂ nanocapsules. Graphitised nanofibres (GNF) were initially filled with iron(III) acetylacetonate, and used as a precursor for the synthesis of ultrasmall Fe₃O₄ nanoparticles (4.6 nm in diameter) inside the cavities of GNF (Fe₃O₄@GNF) with a high density. By using a silica coating process, Fe₃O₄@GNF@SiO>₂ nanocapsules were obtained. The presence of the silica shell not only prevented leakage of the nanoparticles from inside the GNF but also protected the magnetite nanoparticles from dissolution, even in harsh acidic conditions. Furthermore, the silica coating resulted in an increased dispersability of the nanocomposites in water. Magnetic resonance imaging (MRI) studies indicate relatively high  relaxivities for Fe₃O₄@GNF nanocomposites and Fe₃O₄@GNF@SiO>₂ nanocapsules revealing the potential application of these hybrid materials for bioimaging. Therefore, the coating of filled GNF with silica is as an excellent strategy for the protection of encapsulated payloads.