Quercetin (Qu), as an essential flavonoid in plants with antioxidant properties, scavenges environmental stress-induced ROS. Quercetin-based nanocomposites (QNCs) with the same and adequate properties were designed and synthesized for effective Qu delivery in Ocimum basilicum. QNCs were synthesized using the coacervation method, and their effect on the growth, physiological, biochemical, and phytochemical traits of O. basilicum under salinity stress was investigated. Various treatments, including selected concentrations of Qu (0.01 mg/mL) and QNCs (0.01 mg/mL), and four concentrations of NaCl (0, 50, 100, 150 mM) at the vegetative stages, were applied. Results showed that stress markers (Electrolyte leakage, malondialdehyde, hydrogen peroxide) increased with increasing salinity levels. Conversely, salinized plants showed a reduction in plant growth parameters (seed germination, root and shoot length, fresh and dry weight of shoot and root, and plant height) and physiological and photosynthetic parameters (Relative water content, photosynthesis rate, stomatal conductance, photosynthetic pigments, and chlorophyll fluorescence), while application of Qu and QNCs increased these critical parameters. Furthermore, Qu and QNCs enhanced O. basilicum’s tolerance to salinity by increasing compatible solutes content such as glycine betaine, proline, total free amino acids, and soluble carbohydrates; increasing antioxidant enzyme activity; increasing antioxidants content like anthocyanins, tannins, phenols, and flavonoids; and decreasing proteins content and stress markers in plant tissues. Our study suggests that treatment with Qu and QNCs is an effective strategy that can be used to enhance the salt tolerance of O. basilicum plants, and QNCs treatment had a better effect than treatment with Qu.