El Niño events generate periods of relatively low precipitation, low cloud cover and high temperature over the rainforests of Southeast Asia, but their impact on tree physiology remains poorly understood. Here we use remote sensing and functional trait approaches – commonly used to understand plant acclimation to environmental fluctuations – to evaluate rainforest responses to an El Niño event at a site in northern Borneo. Spaceborne measurements (i.e. NDVI calculated from MODIS data) show the rainforest canopy greened throughout 2015, coinciding with a strengthening of the El Niño event in Sabah, Malaysia, then lost greenness in early 2016, when the El Niño was at its peak. Leaf chemical and structural traits measured for mature leaves of 65 species (104 branches from 99 tree canopies), during and after this El Niño event revealed that chlorophyll and carotenoid concentrations were 35% higher in mid 2015 than in mid 2016. Foliar concentrations of the nutrients N, P, K and Mg did not vary, suggesting the mineralisation and transportation processes were unaffected by the El Niño event. Leaves contained more phenolics, tannins and cellulose but less Ca and lignin during the El Niño event, with concentration shifts varying strongly among species. These changes in functional traits were also apparent in hyperspectral reflectance data collected using a field spectrometer, particularly in the shortwave infrared region. Leaf-level acclimation and leaf turnover could have driven the trait changes observed. We argue that trees were not water limited in the initial phase of the El Niño event, and responded by flushing new leaves, seen in the canopy greening trend and higher pigment concentrations (associated with young leaves); we argue that high evaporative demand and depleted soil water eventually caused leaves to drop in 2016. However, further studies are needed to confirm these ideas. Time-series of vegetation dynamics obtained from space can only be understood if changes in functional traits, as well as the quantity of leaves in canopies, are monitored on the ground.