Phytophthora palmivora-induced root and basal stem rot pose a significant threat to the survival of Soe mandarin plants in East Nusa Tenggara Province, Indonesia. We isolated four Trichoderma species, five Bacillus, and 13 Pseudomonas isolates from the rhizosphere of healthy Soe mandarin. This study pursued two main objectives: (a) assessing the inhibitory capabilities of indigenous Trichoderma spp., Bacillus, and Pseudomonas towards P. palmivora in vitro, and (b) investigating the combined efficacy of Trichoderma spp., Bacillus, and Pseudomonas in controlling P. palmivora in a pot trial. Results revealed that four Trichoderma species (T. asperellum, T. hamatum, T. harzianum, and T. viride) significantly inhibited the growth of P. palmivora. Notably, T. asperellum exhibited the highest inhibition, at 84.31%, followed closely by T. harzianum (84.11%), T. viride (83.67%), and T. hamatum (80.28%). Bacillus and Pseudomonas exhibited varying levels of inhibition to P. palmivora growth in vitro, with the most substantial inhibition observed in Bacillus 1, followed by Pseudomonas 6. In the subsequent pot trial, the application of Trichoderma, Bacillus, or Pseudomonas, either individually or in combination, significantly increased the height increment and reduced the disease incidence caused by P. palmivora in Soe mandarin seedlings.