Medicinal and aromatic plants (MAPs) possess phytoremediation potential owing to antioxidants, secondary metabolites, and morphological features. Moringa oleifera, Pelargonium graveolens, Tagetes patula, and Calotropis gigantea are known for their phytoremediation properties in heavy metals polluted soil. These plants with phytoremediation properties due to antioxidants, specific secondary metabolites synthesis, and distinctive morphological characteristics ultimately become the ideal choice for effective remediation. The main aim of the current study is to provide a genetic evaluation using bioinformatics techniques, antioxidant compounds, metabolites, and their activity. Genomic and transcriptomic studies endorsed genes related to hyperaccumulation in these plant species having essential domains as catalase (CAT) and superoxide dismutase (SOD_Cu, SOD_Fe_C, and SOD_Fe_N). The phylogenetic study showed its close evolutionary relationship to other plant species. The accumulation of total photosynthetic pigments, carotenoids, non-enzymatic antioxidants, and enzymatic antioxidants determined spectrophotometrically, involved in stress tolerance and ROS homeostasis maintenance mechanisms. Tagetes leaves showed the highest proline, flavonoids, and phenolics content, while Moringa showed higher CAT, guaiacol peroxidase (G-POD), and glutathione peroxidase (GPX) activities. Results also revealed that plants accumulated more primary and secondary metabolites in young tissue to tackle pathogens, herbivores, attract pollinators, and in mature tissues to develop strong physiology. Total antioxidant activity, reducing power, and radical scavenging activities were observed. These MAPs have intriguing antioxidant characteristics and a phytochemical composition that might give scientific support for their stress tolerance and ROS management activities. The study establishes the groundwork for using MAPs as phytoremediators; further confirmatory research is required for their use in sustainable phytoremediation.