Melatonin, a versatile biomolecule, profoundly influences plant growth and resilience through its intricate regulation of metabolic pathways, circadian rhythms, and cellular processes. The current study elucidates melatonin's concentration-dependent biphasic effects on growth dynamics in Arabidopsis thaliana and Brassica nigra. While 50 μM melatonin optimized biomass accumulation and root elongation, higher concentrations (100 μM) elicited stress responses, underscoring its dual role as a growth promoter and stress modulator. Melatonin extended photosynthetic efficiency by modulating chlorophyll and carotenoid synthesis diurnally, offering protection against photodamage. Divergent responses between the two species, driven by species-specific metabolic reprogramming, were evident in pigment biosynthesis and antioxidant pathways. B. nigra displayed robust activation of flavonoid and phenylpropanoid pathways, cytokinin signaling, and enhanced oxidative defenses, contrasting with A. thaliana, where melatonin suppressed pigment precursors and antioxidant activation. Metabolomic analysis revealed melatonin's orchestration of hormonal crosstalk, involving auxins, gibberellins, and jasmonates, to fine-tune growth and stress adaptation. Stomatal dynamics and cell wall fortification in B. nigra highlighted melatonin's role in optimizing water-use efficiency and structural resilience under abiotic stress. Cytogenetic studies confirmed melatonin's role in safeguarding genomic integrity, regulating chromatin remodeling, and promoting DNA repair mechanisms, with B. nigra demonstrating adaptive genomic strategies under stress. Moreover, melatonin influenced critical metabolic pathways, including polyamine biosynthesis, sulfur metabolism, and nucleotide regulation, emphasizing its multifaceted impact on cellular homeostasis. These findings position melatonin as a cornerstone molecule in plant biotechnology, with potential applications in enhancing crop resilience and productivity under fluctuating environmental conditions.