ABSTRACT The non-photosynthetic vegetation – soil separation index (NSSI) and normalized difference vegetation index (NDVI) can be used to simultaneously estimate the fractional cover of non-photosynthetic vegetation (fNPV), photosynthetic vegetation (fPV), and bare soil (fBS) in vegetation ecosystems. However, these estimates suffer from problems due to shading by dense vegetation or topography. Based on field-measured data and on hyperspectral data acquired by unmanned aerial vehicles, we analyse how shading affects the morphology of NDVI-NSSI and enhanced vegetation index – NSSI (EVI-NSSI). We also investigate the simultaneous estimation of fNPV, fPV, and fBS. The results show that the NDVI-NSSI normalized difference feature space mitigates the impact of shade. Shade causes the NDVI-NSSI and EVI-NSSI to shift rightward parallel to the BS axis and leftward parallel to the PV axis, respectively. Although such shifts may hinder the determination of NPV, PV, and BS endmembers, they do not affect the spectral separation of NPV. Overall, with the NDVI-NSSI and EVI-NSSI methods, the estimation error for fNPV under shaded conditions is approximately 5% greater than that under illuminated conditions. Shaded green vegetation more strongly affects the estimation error of fPV and fBS in EVI-NSSI than in NDVI-NSSI, whereas fBS and fPV depend more strongly on shade than fNPV.