1. Conversion of rainforest into agricultural land affects multiple facets of tropical plant diversity. While the effects of tropical land use change and intensification on species diversity are comparatively well studied, the effects on phylogenetic diversity and structure of plant communities are largely unknown. Furthermore, it is not clear how the loss of native species and addition of alien species collectively affect phylogenetic diversity and structure. 2. We investigated the phylogenetic diversity and structure of understorey plants; a diverse and ecologically important, yet poorly studied group. We studied four prominent land use systems (tropical lowland rainforest, jungle rubber agroforest, rubber plantations and oil palm plantations) in the lowlands of Sumatra (Indonesia), a region experiencing dramatic land use changes. 3. Across the four systems, we investigated differences in four metrics of phylogenetic community structure (phylogenetic diversity, mean pairwise distance, mean nearest taxon distance and their abundance-weighted variants). Our analyses were based on a comprehensive vegetation survey consisting of 32 plots, 1,197 species of vascular plants, and 146,599 plant individuals. 4. Our results showed that forest conversion into agricultural systems leads to a pronounced loss of phylogenetic diversity. Furthermore, the standard effect size of mean pairwise distance indicated a gradual change from clustered to overdispersed phylogenetic community structure with increasing land use intensity from forest over jungle rubber to the monoculture plantations. In most land use systems, the presence or absence of alien plant species did not affect phylogenetic structure. Only in oil palm plantations, removing alien species from the data led to a more overdispersed structure. In conclusion, conserving the phylogenetic diversity and structure requires efficient protection of the last remaining rainforests. 5. Synthesis and applications. Forest conversion into agricultural areas negatively affects phylogenetic understorey plant diversity and leads to a shift from clustered to overdispersed phylogenetic community structure. These trends are partly driven by alien species particularly in oil palm plantations. Protecting the remaining rainforests, and considering multi-species agroforestry systems in favour of intensive monoculture plantations are thus imperative to conserve phylogenetic plant diversity and community structure.