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Abstract Background Exploring the therapeutic potential of unutilized plant parts from agricultural crops represents a promising strategy for discovering novel medications with high positive economic value. This study aimed to characterize the composition, antidiabetic, anti-obesity, antioxidant, and cytotoxic effects of volatile oil (VO) extracted from the leaves of Citrus japonica trees. This is the first research to assess the C. japonica VO’s anti-obesity, anti-lipase, and cytotoxic properties. Using 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) assays and gas chromatography–mass spectrometry (GC–MS) analysis, the components of VO and its capacity to suppress the growth of cancer and other abnormal cells were ascertained, respectively. Stable 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radicals, p-nitrophenyl butyrate (PNPB), and dinitrosalicylic acid (DNSA) assays were employed to determine antioxidant, anti-obesity, and antidiabetic activities, respectively. Results The C. japonica leaf showed significant diversity in type and percentage of VO molecules. Overall, 45 compounds were identified in the VO, constituting 99.69% of the total oil composition. γ-Muurolene (28.12%), β-eudesmol (10.93%), γ-eudesmol (8.44%), germacrene B (7.39%), and elemol (7.27%) are the major characterized molecules. According to the inhibition percentage results of DPPH free radicals, porcine pancreatic lipase, and α-amylase, the VO exhibits strong antioxidant properties and weak inhibitory effects on lipase and α-amylase enzymes. The C. japonica VO showed a moderate cytotoxic effect against Hep3B and considerable activity on B16F1, CaCo-2, HeLa, MCF-7, and HepG2, with IC50 doses in the range of 69.7–171.96 µg/mL. The VO cytotoxic effect IC50 against the normal cell line LX-2 was 224.95 µg/mL. Conclusion The current study collectively presented the chemical constituents of C. japonica leaf VO from Palestine for the first time and demonstrated its inhibitory effects against DPPH free radicals, porcine pancreatic lipase, and α-amylase. The results suggest that C. japonica leaf VO has the potential to be used as a natural supplement to prevent or treat cancer, as well as in the food industry as a natural antioxidant. Graphical Abstract |