On the 29th of October 2018, a storm named “Vaia” hit North-Eastern Italy, causing the loss of 8 million m3 of standing trees and creating serious damage to the forested areas, with many economic and ecological implications. This event brought up the necessity of a standard procedure for windthrow detection and monitoring based on satellite data as an alternative to foresters’ fieldwork. The proposed methodology was applied in Carnic Alps (Friuli Venezia Giulia, NE Italy) in natural stands dominated by Picea abies and Abies alba. We used images from the Sentinel-2 mission: 1) to test vegetation indices performance in monitoring the vegetation dynamics in the short period after the storm, and 2) to create a windthrow map for the whole Friuli Venezia Giulia region. Results showed that windthrows in forests have a significant influence on visible and short-wave infrared (SWIR) spectral bands of Sentinel-2, both in the short and the long-term timeframes. NDWI8A and NDWI were the best indices for windthrow detection (R2 = 0.80 and 0.77, respectively) and NDVI, PSRI, SAVI and GNDVI had an overall good performance in spotting wind-damaged areas (R2 = 0.60–0.76). Moreover, these indices allowed to monitor post-Vaia forest die-off and showed a dynamic recovery process in cleaned sites. The NDWI8A index, employed in the vegetation index differencing (VID) change detection technique, delimited damaged areas comparable to the estimations provided by Regional Forest System (2545 ha and 3183 ha, respectively). Damaged forests detected by NDWI8A VID ranged from 500 m to 1500 m a.s.l., mainly covering steep slopes in the south and east aspects (42% and 25%, respectively). Our results suggested that the NDWI8A VID method may be a cost-effective and accurate way to produce windthrow maps, which could limit the risks associated with fieldwork and may provide a valuable tool to plan tree removal interventions in a more efficient way.