Isodon rugosus Wall. ex Benth (IR) is one of the ethnomedicinal important plants of Gilgit-Baltistan, Northern Pakistan. The present study aims to evaluate the micro-morphological features, phytochemical screening, and pharmacological potential of IR. SEM and LM were used as an identification tool. Five different solvents were used to prepare IR extracts.  Phytochemical and antioxidant activities were determined calorimetrically. To investigate antidiabetic, α-amylase inhibition assay was adopted. Cytotoxicity was tested using a brine shrimp assay. Anti-leishmanial via MTT assay. Disc-diffusion assay was used for protein kinase inhibitory, antibacterial, and antifungal activities. Pollen was of monad, hexacolporate, and circular shape. Lophate sculpturing with outer exine pattern elevated on the rides. Seeds were oblong-ovate, small projected with smooth-rough, variously ridges/wrinkled sculpturing. Epidermis cells were irregular in shape with a slightly straight anticlinal wall. Stomata with diacytic, and unicellular glandular trichome were observed. The extracts were rich in phytochemicals, the maximum amount of phenolic and flavonoid contents was found in methanol extract (IRM) 89.76mg GAE/gm and 85.69mg QE/gm. All the extracts show substantial antioxidant activity but highest in IRM (DPPH IC₅₀ 44.51 µg/ml, total antioxidant capacity 93.60 mg AAE/g, and total reduction power of 93.44 mg AAE/g). Potential antibacterial and antifungal activities were reported for IRM. Significant protein kinase, alpha-amylase inhibition, and cytotoxic activity were revealed. Dose‐dependent cytotoxic activity was exposed against Leishmania tropica (LC₅₀ 11.16 μg/mL). In conclusion, I. rugosus extracts have shown potential biological applications and should be subjected to further research work to develop further biomedical applications.