Raman spectroscopy has been used to monitor the deformation of natural cellulose whisker polymer nanocomposites. Cotton and tunicate whiskers were used as reinforcements in polymer matrices. Raman spectra from the nanocomposites highlight an intense band located at the 1095 cm-1 position. This band is reported to shift towards a lower wavenumber under the application of tensile deformation. On the other hand, the compressive deformation of the composite gives rise to an increase in the position of this Raman band. The shifts correspond to the direct deformation of the molecular backbone of cellulose, which is dominated by a C-O stretching mode. The Raman band located at 1095 cm-1 is shown to shift non-linearly before it reaches a plateau due to the breakdown of the whisker-matrix interface. The initial shift rate is associated with the stiffness of the cellulose whiskers. The stiffnesses of single whiskers of cotton and tunicate are found to be 58 and 155 GPa respectively, assuming two dimensional (2D) in-plane distribution of whiskers. Cyclic deformation tests of the composites provide an insight into understanding the behaviour of the whisker-polymer matrix interface under tension and compression. It is found that residual compressive stress occurs during each cycle of the deformation. The level of disruption at the whisker-matrix interface is determined by estimating the energy dissipation, which is proportional to the hysteresis area. Local orientation is also observed in the nanocomposites produced by solution casting and subsequent melt pressing. Dark regions of the composites viewed under a polarised optical microscopy are found to represent areas in which the cellulose whiskers form a randomly oriented whisker network. A shift rate for the Raman band initially located at 1095 cm-1 obtained in the dark regions of 12.2 vol% tunicate whisker poly(vinyl acetate) nanocomposites is found to be -0.5±0.07 cm-1%-1, which is lower than -1.2±0.04 cm-1%-1 from the bright regions. Exposure to water and temperature during the deformation of the nanocomposites results in significant changes in stress transfer between the whiskers and the matrix. It is shown that the interface can be "switched-off" for the poly(vinyl acetate)/whisker system in the presence of water and also at temperature above the glass transition.