Climate change models predict more frequent and severe droughts in the humid tropics. How drought will impact tropical forest carbon and greenhouse gas dynamics is poorly understood. Here we report the effects of the severe 2015 Caribbean drought on soil moisture, oxygen, phosphorus (P), and greenhouse gas emissions in a humid tropical forest in Puerto Rico. Drought significantly decreases inorganic P concentrations, an element commonly limiting to net primary productivity in tropical forests, and significantly increases organic P. High-frequency greenhouse gas measurements show varied impacts across topography. Soil carbon dioxide emissions increase by 60% on slopes and 163% in valleys. Methane (CH4) consumption increases significantly during drought, but high CH4 fluxes post-drought offset this sink after 7 weeks. The rapid response and slow recovery to drought suggest tropical forest biogeochemistry is more sensitive to climate change than previously believed, with potentially large direct and indirect consequences for regional and global carbon cycles.