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Calligonum polygonoides , a desert shrub used in folk medicine has been suggested to possess pharmacological potential. However, its anticancer and antidiabetic properties have not been validated. This study aimed to evaluate the anticancer and antidiabetic potential of C. polygonoides through bioassay-guided fractionation with in vitro , in vivo and in silico approaches. The study involved phytochemical profiling, enzymatic assays, cell culture experiments, animal models and docking analyses. The ethanolic extracts from roots, stems, and flowers of C. polygonoides were fractionated and characterized. The anticancer activity was assessed in HepG2 and Vero cell lines using MTT and morphological assays where cisplatin was used as positive and untreated HepG2 cells as negative control. The antidiabetic activity was determined in vitro by α-amylase and α-glucosidase inhibition assays, followed by the in vivo validation in alloxan-induced diabetic rats. The LC–MS profiling tentatively identified secondary metabolites, which were subjected to docking against CDK-1 and diabetes-related enzymes. The ADME analysis was performed to predict pharmacokinetic and safety profiles. Results indicated that the EtOAc R extract produced moderate cytotoxicity in HepG2 cells (IC₅₀ < 100 μg/mL), and caused morphological changes consistent with cytotoxic stress. The LC–MS analysis of EtOAc R extract identified diverse bioactive compounds including flavonoids, phenolic acids, terpenoids, and lignans. The molecular docking studies revealed strong CDK-1 binding affinities (−8.0 to −10.3 kcal/mol). On the other hand, the ethanolic stems (EtOH S) extract and its VLC fractions ( V9 , V13 ) displayed strong α-amylase and α-glucosidase inhibition, with IC₅₀ values comparable to standard drug acarbose. The in vivo studies confirmed significant reductions in fasting blood glucose in diabetic rats, similar to glibenclamide. The Molecular docking supported strong binding of polyhydroxylated flavonoids to catalytic residues of both enzymes. While, ADME analysis of EtOAc R extract, V9 and V13 fractions indicated favorable gastrointestinal absorption and safety profiles.