Plant invasions can result in serious threats for biodiversity and ecosystem functioning. Reliable maps at very-high spatial resolution are needed to assess invasions dynamics. Field sampling approaches could be replaced by unmanned aerial vehicles (UAVs) to derive such maps. However, pixel-based species classification at high spatial resolution is highly affected by within-canopy variation caused by shadows. Here, we studied the effect of shadows on mapping the occurrence of invasive species using UAV-based data. MaxEnt one-class classifications were applied to map Acacia dealbata, Ulex europaeus and Pinus radiata in central-south Chile using combinations of UAV-based spectral (RGB and hyperspectral), 2D textural and 3D structural variables including and excluding shaded canopy pixels during model calibration. The model accuracies in terms of area under the curve (AUC), Cohen’s Kappa, sensitivity (true positive rate) and specificity (true negative rate) were examined in sunlit and shaded canopies separately. Bootstrapping was used for validation and to assess statistical differences between models. Our results show that shadows significantly affect the accuracies obtained with all types of variables. The predictions in shaded areas were generally inaccurate, leading to misclassification rates between 65% and 100% even when shadows were included during model calibration. The exclusion of shaded areas from model calibrations increased the predictive accuracies (especially in terms of sensitivity), decreasing false positives. Spectral and 2D textural information showed generally higher performances and improvements when excluding shadows from the analysis. Shadows significantly affected the model results obtained with any of the variables used, hence the exclusion of shadows is recommended prior to model calibration. This relatively easy pre-processing step enhances models for classifying species occurrences using high-resolution spectral imagery and derived products. Finally, a shadow simulation showed differences in the ideal acquisition window for each species, which is important to plan revisit campaigns.