Tropical cyclone (TC) Seroja was a rare climatic event in the Indonesian Seas, particularly in the Savu Sea. This unprecedented event, which occurred on April 4, 2021, caused fatalities and severe damage to the region’s infrastructure and economy. High spatio-temporal resolution satellite measurements of surface winds (Cross-Calibrated Multi-Platform), surface chlorophyll-a (Himawari-8), and sea surface temperature (SST; RSS OISST) are used to disentangle the impact of extreme wind speed (<inline-formula> <tex-math notation="LaTeX">$>10\,\,\text{m}\cdot \text{s}^{-1}$ </tex-math></inline-formula>) on chlorophyll-a and SST. High wind speed associated with TC Seroja induced strong upwelling and vertical mixing in the Savu Sea, which led to phytoplankton blooms and SST depression. An abrupt change of daily variability and positive anomaly in phytoplankton chlorophyll-a concentrations reaches 13 mg<inline-formula> <tex-math notation="LaTeX">$\cdot \text{m}^{-3}$ </tex-math></inline-formula> and 0.3 mg<inline-formula> <tex-math notation="LaTeX">$\cdot \text{m}^{-3}$ </tex-math></inline-formula>, respectively. At the same time, the SST shows significant cooling up to 3°C. Our results provide novel insights on the exceptional occurrence of a TC within the Indonesian Seas and highlight its impact on chlorophyll-a and SST.