Visible and near-infrared spectroscopy have been widely used for non-destructive and rapid monitoring of biological materials including agricultural produce and foods. Methods for decomposition of spectra of biological materials into that of each layer are demanded because the target of monitoring is in most cases limited to a single layer (e.g. sweetness of the flesh of a fruit, not the skin). Also, separation of light absorption and scattering properties is considered to lead more robust modeling of biological materials. Therefore, the potential of Parallel factor analysis (PARAFAC) on spatially resolved spectroscopy (SRS) has been investigated in this study. Spatially resolved spectra of 120 ?Braeburn? apples with difference in skin color (green and red) and storage condition (before and after 14 days shelf-life storage) were measured in the 400-1100 nm range using 7 detection fibers with different source-detector distance. PARAFAC on the whole data set could decompose the spatially resolved spectra into that of flesh and skin as factor 1 and 2 wavelength loadings, respectively. This result was validated by the facts that the factor 1 loading was almost identical to the ?real? spectra of flesh, which had been acquired by measuring peeled apples, and peaks observed in the factor 2 loading corresponded to absorption bands of pigments contained in apple skin. When PARAFAC was applied to individual sample data sets, difference in skin color and chlorophyll content as well as degradation of chlorophyll in skin during ripening and storage could be modelled as the change in factor 1 wavelength loading. These results support the potential of SRS combined with PARAFAC to decompose the spectra of multi-layered biological materials.