AbstractThe rapidly growing areal extent of oil palm (Elaeis guineensis Jacq.) plantations and their high fertilizer input raises concerns about their role as substantial N2O sources. In this study, we present the first eddy covariance (EC) measurements of ecosystem‐scale N2O fluxes in an oil palm plantation and combine them with vented soil chamber measurements of point‐scale soil N2O fluxes. Based on EC measurements during the period August 2017 to April 2019, the studied oil palm plantation in the tropical lowlands of Jambi Province (Sumatra, Indonesia) is a high source of N2O, with average emission of 0.32 ± 0.003 g N2O‐N m−2 year−1 (149.85 ± 1.40 g CO2‐equivalent m−2 year−1). Compared to the EC‐based N2O flux, average chamber‐based soil N2O fluxes (0.16 ± 0.047 g N2O‐N m−2 year−1, 74.93 ± 23.41 g CO2‐equivalent m−2 year−1) are significantly (~49%, p < 0.05) lower, suggesting that important N2O pathways are not covered by the chamber measurements. Conventional chamber‐based N2O emission estimates from oil palm up‐scaled to ecosystem level might therefore be substantially underestimated. We show that the dynamic gas exchange of the oil palm canopy with the atmosphere and the oil palms' response to meteorological and soil conditions may play an important but yet widely unexplored role in the N2O budget of oil palm plantations. Diel pattern of N2O fluxes showed strong causal relationships with photosynthesis‐related variables, i.e. latent heat flux, incoming photosynthetically active radiation and gross primary productivity during day time, and ecosystem respiration and soil temperature during night time. At longer time scales (>2 days), soil temperature and water‐filled pore space gained importance on N2O flux variation. These results suggest a plant‐mediated N2O transport, providing important input for modelling approaches and strategies to mitigate the negative impact of N2O emissions from oil palm cultivation through appropriate site selection and management.