Tropical cyclones (TCs) are natural systems that develop over ocean basins and are key components of the atmospheric activity during the warm season. However, there are still knowledge gaps about the combined positive and negative TC impacts on the structure and function of coastal socio-ecosystems. Using remote sensing tools, we analyzed the frequency, trajectory, and intensity of 1894 TCs from 1851–2019 to identify vulnerable “hotspots” across the Yucatan Peninsula (YP), Mexico. A total of 151 events hit the YP, with 96% of landings on the eastern coast. We focused on three major hurricanes (Emily and Wilma, 2005; Dean, 2007) and one tropical storm (Stan, 2005) to determine the impacts on cumulative precipitation, vegetation change, and coastal phytoplankton (Chl-a) distribution across the YP. Despite a short inland incursion, Wilma’s environmental damage was coupled to strong winds (157–241 km/h), slow motion (4–9 km/h), and heavy precipitation (up to 770 mm). Because of an extensive footprint, Wilma caused more vegetation damage (29%) than Dean (20%), Emily (7%), and Stan (2%). All TCs caused a Chl-a increase associated to submarine discharge and upwelling off the peninsula coastlines. Disaster risk along the coast underscores negative economic impacts and positive ecological benefits at the regional scale.