This research examines the long-term toxicity of nano-formulated Bischofia javanica leaves, a medicinal plant widely used in Indonesia, following OECD guideline 452. Mice were administered four different doses (2, 4, 6, and 8 g/kg body weight) of the nano-formulated extract for 60 days, while the control group received only water. On the 61st day, animals were euthanized for the collection of blood and tissue samples for biochemical, hematological, and histopathological evaluation. Data analysis was performed using one-way ANOVA with Tukey’s post hoc test. Low to moderate doses (2–4 g/kg BW) enhanced liver structure and function, whereas higher doses (6–8 g/kg BW) induced liver damage characterized by fat accumulation in hepatocytes, degeneration of central blood vessels, and sinusoidal disruption. Lung tissues in high-dose groups displayed alveolar inflammation, epithelial cell shedding, cellular debris, and infiltration of inflammatory cells. Heart tissue was largely normal at lower doses, but higher doses resulted in hemorrhages and deposition of amorphous material. Apart from elevated liver injury markers at high doses, other hematological and biochemical parameters, including blood glucose, remained largely unaffected, and no treatment-related deaths were observed. Overall, moderate dosing of nano-formulated Bischofia javanica leaves appears to support organ function, but high doses can compromise vital organs, underscoring the need for cautious therapeutic use.