<p>Delineating the tree-associated microbiome uncovers complex interactions that ultimately improve strategies for tree growth, disease resistance, and environmental sustainability. The hemi-parasitic nature and susceptibility to diseases pose significant challenges for proper silviculture operations in <i>Santalum album</i> L. Sandalwood-associated microbiota and their interactions hold considerable potential for applications in conservation and management practices. In the present review, we summarize the current understanding on the rhizosphere and endosphere microbiota present in Indian sandalwood, potential pathogenic threats to the species and how microbiome-based studies can assist in improving agroforestry and conservation efforts. The potential microbial interactions that can monitor and manage forest and ecosystem health, guide restoration strategies, and contribute to species improvement are explored. The utility of current high-throughput sequencing technologies and approaches to unravell the microbial diversity and composition, as well as determine the functional capacities of microbes, is analysed. Understanding the role of microbes in adaptation sheds light on how shifts in microbial communities help trees improve their resilience to climate change. We aim to identify the potential gaps in sandalwood microbiome research and explore how addressing these gaps can contribute to the conservation and sustainable management of the species, broader forest ecosystems, and improve present agroforestry practices. The review concludes by discussing how these findings can be applied to design and manage agroforestry trials that promote the sustainability of sandalwood resources along with other cropping systems.</p>