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In this study, composite nanofibres were fabricated from solvent fractionated softwood kraft lignin (SKL), NCC and polyethylene oxide (PEO) by electrospinning. The molecular organization of lignin was investigated in the form of spun fibres and films with and without NCC. Subsequently, the as-spun composite nanofibre mats were thermally stabilized in the air under controlled conditions. The chemical and mechanical properties were studied as a function of the processing conditions. The oxidized nanofibres were then carbonized at 1000 ºC in inert nitrogen atmospheres. The responses investigated include changes in yield, diameter/distribution of nanofibres, thermal stability, elemental composition, the molecular structure and mechanical properties. Lastly, effects of NCCs on lignin structure in the fibres at different stages of heat treatments were determined. Lignin molecules demonstrated organization within aligned electrospun fibres and within solvent cast lignin films. The nanofibres and films of lignin with and without NCC had birefringence as revealed with polarized optical microscope. Also, through heat treatment, the lignin-based nanofibres mats with or without NCC, showed improved mechanical and thermal-chemical properties after thermal stabilization and carbonization processes. Specifically the properties of thermally stabilized samples were more variable than carbonized samples. Furthermore, NCC loadings gave a significant reduction in mobility of lignin molecules during heat treatment allowing for direct carbonization for lignin carbon fibres production with NCC loadings for 5 wt.%. NCC overall did not enhance the mechanical properties of the electrospun fibre. However significant interactions between the NCC and lignin were revealed with FTIR spectroscopy and thermal rheological analysis. In summary, the work investigated how thermal treatments can enhance the performance of lignin-based materials and further enhanced by the presence of nanofillers. This study investigated extensively the effect of NCC in lignin-based composite nanofibres through fundamental understanding of the interaction between lignin and NCC during the different heat treatment stages for carbon fibre production.