The 2015–2016 El Niño caused severe droughts in tropical forests, but its impact on the Cerrado, Brazil's largest savanna, was unclear. Our study tracked the productivity of two key Cerrado vegetation types over 5 years. Before the El Niño, productivity was higher in the transitional forest–savanna, but it dropped sharply during the event. Meanwhile, the savanna showed minor changes. These findings suggest that transitional ecosystems are particularly vulnerable to drought and climate change.