The diverse lowland forests of Southeast Asia and Borneo are globally recognised biodiversity hotspots containing rare and endangered species and high levels of plant endemism. Heath and peat swamp forests are Bornean lowland forest types with distinctive plant communities that primarily correspond to a soil water gradient from dryland heath to waterlogged peat swamps. Although tree diversity of Bornean heath and peat swamp forests is well described, little is known of their woody seedling communities. This study investigated diversity, abundance and community composition of woody seedlings in mixed peat-swamp (MSF), heath (HF), kerapah (KF) and Shorea albida peat-swamp (SAP) forests in Brunei Darussalam, Northwest Borneo. Within twenty-two 3 × 3 m plots in these forest types, seedlings of 50 ≤ cm height ≤ 100 were censused and taxonomically identified, and measurements of selected environmental and soil properties were obtained. In total, 84 species of woody seedlings from 71 genera were recorded, with Myrtaceae most abundant in MSF, KF and SAP, while Dipterocarpaceae and Sapotaceae were most abundant in HF. Mean seedling abundance and diversity indices did not differ between forest types, but mean species richness was significantly higher in MSF than SAP. Woody seedling community composition differed between forest types and was influenced by soil properties, with MSF seedling communities influenced by total K concentration and soil pH, while SAP was influenced by soil gravimetric water content and total P concentration. These findings highlight the need for increased research on seedling ecology in tropical heath and peat swamp forest formations to further elucidate mechanisms underlying species diversity in these forests, and to guide programmes for their conservation, sustainable management and reforestation.