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To test whether plant species influence greenhouse gas production in diverse ecosystems, we measured wet season soil CO₂ and N₂O fluxes close to ∼300 large (>35 cm in diameter at breast height (DBH)) trees of 15 species at three clay‐rich forest sites in central Amazonia. We found that soil CO₂ fluxes were 38% higher near large trees than at control sites >10 m away from any tree (P < 0.0001). After adjusting for large tree presence, a multiple linear regression of soil temperature, bulk density, and liana DBH explained 19% of remaining CO₂ flux variability. Soil N₂O fluxes adjacent to Caryocar villosum, Lecythis lurida, Schefflera morototoni, and Manilkara huberi were 84%−196% greater than Erisma uncinatum and Vochysia maxima, both Vochysiaceae. Tree species identity was the most important explanatory factor for N₂O fluxes, accounting for more than twice the N₂O flux variability as all other factors …