Declines of large vertebrates in tropical forests may reduce dispersal of tree species that rely on them, and the resulting undispersed seedlings might suffer increased distance‐ and density‐dependent mortality. Consequently, extirpation of large vertebrates may alter the composition and spatial structure of plant communities and impair ecosystem functions like carbon storage. We analysed spatial patterns of tree recruitment within six forest plots along a defaunation gradient in western Amazonia. We divided recruits into two size cohorts (“saplings”: ≥1 m tall and <1 cm diameter at breast height [dbh], and juveniles, 1–2 cm dbh) and examined the spatial organisation of conspecific recruits within each cohort (within‐cohort) and around conspecific reproductive‐sized trees (between‐cohort). We used replicated spatial point pattern analysis to quantify relationships between recruit clustering and cohort, defaunation intensity, each tree species reliance on hunted dispersers and the interactions among these three covariates. Within‐cohort clustering of conspecific saplings increased with reliance of tree species on hunted dispersers, and this trend strengthened significantly as defaunation increased, probably because of reduced dispersal. Within‐cohort clustering of conspecifics declined from saplings to juveniles, suggesting density‐dependent mortality of saplings. However, the positive relationship between sapling clustering and defaunation did not lead to greater reductions in within‐cohort clustering during the sapling–juvenile transition, suggesting that higher conspecific densities did not translate into increased mortality. Instead, the increased spatial clustering associated with defaunation was retained for juvenile recruits. Between‐cohort clustering was unrelated to defaunation and did not change during the sapling–juvenile transition. Synthesis. Defaunation increased spatial aggregation of saplings of tree species reliant on hunted dispersers. The increase in sapling clustering did not increase density‐dependent thinning, and persisted into older recruit cohorts, suggesting that hunting may initiate long‐term spatial reorganisation of Amazonian tree communities. The lack of increased density‐dependent thinning indicates that reduced dispersal did not increase mortality of large‐vertebrate dispersed tree species that contribute disproportionately to forest biomass. We, therefore, caution against the fait accompli acceptance of the prediction by recent modelling studies that overhunting will precipitate a collapse in carbon sequestration by tropical forests.