Attributing the extent of changes in vegetation cover which are the result of human actions or of climate variability is challenging. The Negev Desert, bordered by two countries and the Palestinian Authority and crossing three climate zones, provides a natural laboratory for unveiling the impact of land practices on natural vegetation. Desert vegetation on both sides of the border was traditionally subject to herds grazing and bush gathering, but in recent decades; grazing policy, military training areas, and nature protection have excluded traditional uses. We used remotely sensed derived proxies of vegetation (the Normalized Difference Vegetation Index) and surface albedo from satellite images inside and outside of the large exclosures to estimate the anthropogenic impact on vegetation cover in the past four decades, and ultimately isolate the effect of traditional land uses on vegetation cover. Our results showed that the cross-border differences in land use led to a significant impact on vegetation cover outside the exclosed areas. These cross-border differences were more pronounced in the semi-arid - arid climate regions and decreased in the hyper-arid climate region. Exclosures provide a natural experiment which enables us the testing of the factors driving changes in natural vegetation. •We analyzed the impact of exclosures (borders and army bases) on desert vegetation.•We quantified proxies of vegetation cover using time series of MODIS and Landsat.•Cross-fence differences in traditional land use significantly impacted vegetation.•Cross-fence differences decreased in the hyper-arid climate region.