The use of drones for vegetation monitoring allows the acquisition of large amounts of high spatial resolution data in a simple and fast way. In this study, we evaluated the accuracy of vegetation cover estimation by drones in Mediterranean semi-arid shrublands (Sierra de Filabres; Almería; southern Spain) after prescribed burns (2 years). We compared drone-based vegetation cover estimates with those based on traditional vegetation sampling in ninety-six 1 m2 plots. We explored how this accuracy varies in different types of coverage (low-, moderate- and high-cover shrublands, and high-cover alfa grass steppe); as well as with diversity, plant richness, and topographic slope. The coverage estimated using a drone was strongly correlated with that obtained by vegetation sampling (R2 = 0.81). This estimate varied between cover classes, with the error rate being higher in low-cover shrublands, and lower in high-cover alfa grass steppe (normalized RMSE 33% vs. 9%). Diversity and slope did not affect the accuracy of the cover estimates, while errors were larger in plots with greater richness. These results suggest that in semi-arid environments, the drone might underestimate vegetation cover in low-cover shrublands.