Oil palm contributes to various global needs as one of the most productive oil crops, but there exist ongoing concerns regarding its yield reductions and associated environmental impacts resulting from land conversion. This is the first detailed report investigating the nonlinear threats to estate-level oil palm yields posed by El Niño Southern Oscillation (ENSO) in the equatorial Pacific Ocean, a major driver of climate variability. Using the Malaysian Palm Oil Board administrative records on monthly performances reported by oil palm estates through the e-submissions portal spanning from January 2015 to June 2023, we focused on elucidating the impacts of ENSO on fresh fruit bunch yield, oil extraction rate, and oil yield. We found that both El Niño and La Niña conditions, characterized by extreme levels of ENSO indices cumulated over lags of 0–23 months prior to harvest, were associated with statistically significant reductions in yields. Lag association patterns unveiled that production risks were linked to pre-harvest exposure to extreme ENSO indices in various time windows. Subgroup analyses further revealed that the effects were pronounced in labor-intensive estates and those lacking fertilizer investments. This study underscores the necessity for adaptation strategies in response to future climate anomalies.