The study assessed the efficacy of parsley and dill essential oils (EOs) nanocapsules incorporated into fermented milk in hepato-renal protection against specific food additives. A molecular docking assay was conducted between parsley and dill EOs bioactive molecules and inflammatory cytokines. Freeze-dried parsley and dill EOs nanocapsules were developed, characterized for their morphological structure, particle size, zeta potential, polydispersity index and encapsulation efficiency and assessed in fast green dye and sodium benzoate (SB) combination-treated rats. The docking results revealed that the primary constituents of parsley and dill EOs (apiol, myristicin, α-pinene, (−)-carvone, and d-limonene) interacted with the active sites of TNF-α, IL-1β and TGF-1β cytokines with hydrophobic and hydrogen bond interactions. D-limonene had the highest binding affinity (6.4 kcal/mol) for the TNF-α. Apiol and myristicin had the highest binding affinity (5.1, 5.0, 5.0 and 5.0 kcal/mol, respectively) for the IL-1β and TGF-β1 receptors. Biochemically and histopathologically, the excessive co-administration of fast green and SB revealed adverse effects on the liver and the kidney. Whereas the treatment with parsley and dill EOs nanocapsules afford hepato-renal protective effects as manifested by suppression the elevated liver and kidney functions. Parsley and dill EOs nanocapsules showed a significant reduction of the liver (64.08 and 80.5 pg/g, respectively) and kidney (59.3 and 83.6 pg/g, respectively) ROS. Moreover, parsley and dill EOs nanocapsules down-regulated the liver and the kidney inflammatory cytokines (IL-6, TNF-α, IL-1β and TGF-1β) and lipid peroxidation and up-regulated the antioxidant enzymes. In conclusion, the data suggest a potential hepato-renal protective effects of parsley and dill EOs nanocapsules.