Abstract Natural deep eutectic solvents (NDESs) based on choline chloride (ChCl) together with glycerol (Gly), urea (U), and l-glutamine (L-Gln) were used for the improvement of solubility, stability, and bioactivity of chrysin (CHR). CHR is a promising flavonoid that has multifarious biological activities but a very low water solubility limits its clinical applications. A 21 different NDESs preparation were prepared and evaluated for solubility, pH, and kinematic viscosity. Among the different NDESs prepared, the ChCl: L-Gln: Gly combination gave the optimum solubility of CHR (10.13 ± 1.1 mg/mL). Motic microscopy and Differential scanning calorimetry revealed a transition in the crystalline nature of CHR in NDESs. Furthermore, FTIR and 1NMR were used to investigate the nature of molecular interaction exhibited by the selected NDESs-CHR preparation. The pH stability studies showed the protective effect of CHR in NDESs at simulated gastric conditions. The in vitro dissolution studies revealed an improvement in the dissolution rate of CHR presented in NDESs, compared to pure CHR. Besides, the in vitro cytotoxicity unveils a significant anti-proliferative activity of NDESs-CHR on Hep-G2 cells. The pharmacokinetic study revealed a 2.13-folds increment in oral bioavailability of CHR in selected NDESs preparation. Therefore, the presented study reports NDESs as a promising carrier considering their biosafety issues for hydrophobic flavonoids which could draw attention in pharmaceutical and food science.