Santalum album is a hemiparasitic plant that obtains some of its water and nutritional requirements by parasitizing the roots of neighboring plants. As a hemiparasite, S. album can obtain organic N from parasitizing host roots as well as inorganic N by absorption thru its roots. In this current study, we evaluated changes in the physiology, transcriptional profiles and chromatin accessibility in S. album seedlings exposed to low N conditions with and without supplemental melatonin. We employed two complementary assays, global transcriptome analysis (RNA-seq) and assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) to identify genes and genic regions differentially regulated in S. album roots under these conditions. Low N conditions disturbed the homeostasis of N metabolism, reducing both N uptake and assimilation. The inclusion of melatonin enabled S. album seedlings in low N conditions to achieve significantly higher levels of N uptake and assimilation compared to plants without melatonin. Interestingly, melatonin treatment also enhanced haustorium development through a mechanism associated with auxin accumulation. These results suggest that the application of supplemental melatonin may accelerate N metabolism and haustorium formation of S. album in low N conditions.