Negatively charged carboxyl groups were introduced onto silk fibroin by using sodium hypochlorite (NaClO) oxidation. The nanofibrillar structure of oxidized silk fibroin (OxSF) was investigated by thioflavin T fluorescence and TEM over time. The fractal dimension (Df) value of 1.21 was obtained in 0.5 wt% OxSF with 2 mM NaClO oxidation (1.09 mM per g protein of carboxyl content), suggesting that the formation of individual nanofibrils was key during aggregation. Moreover, the fractal structure of the resulting nanofibrils was regulated by the charge distribution of OxSF. Df values of 1.68, 1.48 and 1.24 were obtained in 0.2 wt% OxSF with 0.5, 1 and 2 mM NaClO in which the corresponding carboxyl content was 0.58, 0.75 and 1.09 mM per g protein, respectively. Nanoindentation measurements demonstrated reinforced hardness and modulus in OxSF-chitosan composite materials obtained by layer-by-layer deposition, with the highest average values of 1.23 ± 0.06 and 20.01 ± 1.64 GPa, respectively.