AbstractTropical cyclones can physically alter ecosystems, causing immediate and potentially long‐lasting effects on carbon dynamics. In 2018, Hurricane Michael hit the southeastern United States with category 5 winds at landfall and category 2 winds reaching over 100 miles inland, resulting in extensive damage. Longleaf pine woodlands in the path of the hurricane were damaged, but severity varied based on the storm track. We used a combination of eddy covariance measurements, airborne LiDAR, and forest inventory data to determine whether hurricane affects structure, function, and recovery of two longleaf pine woodlands at the ends of an edaphic gradient. We found that the carbon sink potentials in both sites were diminished following the storm, with reductions in net ecosystem exchange (NEE) primarily due to lower rates of photosynthesis, as respiration only increased marginally. The xeric site carbon losses and physiological reductions were smaller following the disturbance, which led to the recovery of ecosystem physiological activity to prestorm rates before that of the mesic site, as indicated by maximum ecosystem CO₂ uptake rates. Two years following the hurricane both stands continued to have reduced NEE, which signaled altered function. We expect both locations to recover their lost carbon stocks in ∼10–35 years; however, long‐term studies are needed to examine how longleaf woodlands respond to compounding disturbances, such as drought, fire, or other wind storms, which vary significantly across the ecosystem's range. Additionally, hurricanes are intensifying due to climate change, potentially amplifying the degree to which they will alter this ecosystem in the future.