It has been suggested that tropical defaunation may unleash community-wide cascading effects, leading to reductions in plant diversity. However, experimental evidence establishing cause–effect relationships thereof is poor. Through a 5 year exclosure experiment, we tested the hypothesis that mammalian defaunation affects tree seedling/sapling community dynamics leading to reductions in understorey plant diversity. We established plot triplets (n = 25) representing three defaunation contexts: terrestrial-mammal exclosure (TE), medium/large mammal exclosure (PE) and open access controls (C). Seedlings/saplings 30–100 cm tall were marked and identified within each of these plots and re-censused three times to record survival and recruitment. In the periods 2010–2011 and 2011–2013, survival was greater in PE than in C plots and recruitment was higher in TE plots than in C plots. Overall, seedling density increased by 61% in TE plots and 23% in PE plots, whereas it decreased by 5% in C plots. Common species highly consumed by mammals (e.g. Brosimum alicastrum and Ampelocera hottlei) increased in their abundance in TE plots. Rarefaction curves showed that species diversity decreased in TE plots from 2008 to 2013, whereas it remained similar for C plots. Given the prevalence of tropical defaunation, we posit this is an anthropogenic effect threatening the maintenance of tropical forest diversity.