Embedding silicon nanoparticles in an intermetallic matrix is a promising strategy to produce remarkable bulk anode materials for lithium-ion (Li-ion) batteries with low potential, high electrochemical capacity and good cycling stability. These composite materials can be synthetized at a large scale using mechanical milling. However, for Si-Ni3Sn4 composites, milling also induces a chemical reaction between the two components leading to the formation of free Sn and NiSi2, which is detrimental to the performance of the electrode. To prevent this reaction, a modification of the surface chemistry of the silicon has been undertaken. Si nanoparticles coated with a surface layer of either carbon or oxide were used instead of pure silicon. The influence of the coating on the composition, (micro)structure and electrochemical properties of Si-Ni3Sn4 composites is studied and compared with that of pure Si. Si coating strongly reduces the reaction between Si and Ni3Sn4 during milling. Moreover, contrary to pure silicon, Si-coated composites have a plate-like mor-phology in which the surface-modified silicon particles are surrounded by a nanostructured, Ni3Sn4-based matrix leading to smooth potential profiles during electrochemical cycling. The chemical homogeneity of the matrix is more uniform for carbon-coated than for oxygen-coated silicon. As a consequence, different electrochemical behaviors are obtained depending on the surface chemistry, with better lithiation properties for the carbon-covered silicon able to deliver over 500 mAh/g for at least 400 cycles.