Influence of carbon coating and silicon initial organization on lithiation of silicon nanoparticles (NPs) is analyzed using electrochemical techniques. Four different silicon based NPs materials have been synthetized and electrochemically characterized: one amorphous and one crystalline uncoated, two coated silicon NPs with different carbon contents. The coating lowers the potential under open circuit conditions during delithiation, without impact on lithiation. Capacity retention is similar for uncoated materials (around 1200 mAh.g−1), while improvement is achieved with the thickest coating (2500 mAh.g−1 after 40 cycles). Analysis of Electrochemical Impedance spectra performed during lithiation enables tracking the evolution of charge transfer and Solid Electrolyte Interphase (SEI) resistances. The presence of carbon coating with the highest content results in a more stable SEI with a lower resistance in accordance with the improved cyclability, while inducing an increase of the charge transfer resistance. Results suggest that the charge transfer resistance and the SEI evolution directly depend on the alloying transformation occurring during lithiation, with a strong increase for a LixSi stoichiometry above x = 2.3. Limitation of material lithiation to Li2.3Si could thus be a strategy to avoid these significant resistances increases, while still providing 2210 mAh.g−1 of theoretical capacity.