Island biodiversity is considered to be particularly vulnerable to biological invasions. However, the direct impacts of invasive alien plants on native and endemic flora are often difficult to assess. Indeed, invasion by woody species is a relatively slow process, and natural or anthropogenic disturbances that favor some plant invaders, also contribute to biodiversity loss, and might act as confounding factors. Hence, we conducted a long-term monitoring of rainforest composition and structure in the small tropical high volcanic island of Moorea (French Polynesia, South Pacific) over a 16-year (2006–2022) period without any major disturbance. All endemic, native and alien woody species with a stem ≥ 1 cm in diameter were identified and measured with a 4-year frequency in ten 20 m × 20 m plots. The variation of species richness, Shannon diversity, Pielou evenness and abundance over time was analyzed using linear mixed-effects models with identities of the plots as random factors. Results revealed an increase in the number of stems of alien plants (+ 50% in 16 years), especially the two most common invasive alien trees, Miconia calvescens (Melastomataceae) and Spathodea campanulata (Bignoniaceae). In contrast, we found a decrease in the richness (from 28 species to 19) and abundance (-20% of stems) of endemic and native species, especially in the higher-elevation plots. Three plots remained relatively stable in terms of plant invasions according to Shannon and Pielou indices, and some common native and endemic woody species persisted over time. Although a continuous decline of plant diversity, including species extirpation, was observed, our results also suggest a relative resilience of certain forest types and associated communities to plant invasions. Efforts to control invasive alien plants should therefore target the most vulnerable native habitats.