Plantations of fast-growing Eucalyptus trees have become a common sight in the western Iberian peninsula where they are planted to exploit their economic potential. Negative side-effects of large scale plantations including the invasive behavior of Eucalyptus trees outside of regular plantations have become apparent. This study uses medium resolution, multi-spectral imagery of the Sentinel 2 satellites to map Eucalyptus across Portugal and parts of Spain with a focus on Natura 2000 areas inside Portugal, that are protected under the European birds and habitats directives. This method enables the detection of small incipient as well as mixed populations outside of regular plantations. Ground truth maps were compiled using field surveys as well as high resolution satellite imagery and were used to train Feedforward Neural Networks. These models predict Eucalyptus tree cover with a sensitivity of up to 75.7% as well as a specificity of up to 95.8%. The overall accuracy of the prediction is 92.5%. A qualitative assessment of Natura 2000 areas in Portugal has been performed and 15 areas have been found to be affected by Eucalyptus of which 9 are strongly affected. This study demonstrates the applicability of multi-spectral imagery for tree-species classification and invasive species control. It provides a probability-map of Eucalyptus tree cover for the western Iberian peninsula with 10 m spatial resolution and shows the need for monitoring of Eucalyptus in protected areas.