The productivity of tropical forests is driven by climate (precipitation, temperature, light) and soil fertility (geology, topography). While large-scale drivers of tropical productivity are well established, knowledge on the sensitivity of tropical lowland net primary production to climate anomalies remains scarce. We here analyze seven consecutive years of monthly-recorded tropical forest aboveground net primary production (ANPP) in response to a recent El Niño Southern Oscillation (ENSO) anomaly. The ENSO transition period resulted in increased temperatures and decreased precipitation during the El Niño dry-period, causing a decrease in ANPP. However, the subsequent La Niña wet-period caused strong increases in ANPP such that drought-induced reductions were overcompensated. Most strikingly, the climatic controls differed between canopy production (CP) and wood production (WP). Whereas CP showed strong seasonal variation but was not affected by ENSO, WP decreased significantly in response to a 3 °C increase in annual maximum temperatures during the El Niño period but subsequently recovered to above pre-drought levels during the La Niña period. Moreover the climate sensitivity of tropical forest ANPP components was affected by local topography (water availability) and disturbance history (species composition). Our results suggest that projected increases in temperature and dry season length could impact tropical carbon sequestration by shifting ANPP partitioning towards decreased WP, thus decreasing the carbon storage of highly productive lowland forests. We conclude that the impact of climate anomalies on tropical forest productivity is strongly related to local site characteristics and will therefore likely prevent uniform responses of tropical lowland forests to projected global changes.