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Methanol and methanol/water extracts of olive stones and seeds from Olea europaea var. meski were analyzed by reversed-phase high-performance liquid chromatography (HPLC) with diode array detection and mass spectrometry (LC-MS/MS). A total of 28 metabolites were identified; among them are hydroxycinnamic acid derivatives, phenolic alcohols, flavonoids and flavonoid glucosides, secoiridoids, and terpenes. All the extracts were screened for the inhibitory effect of key enzymes related to diabetes and obesity, such as α-amylase and lipase. An in vitro study revealed that Olea meski stone ethanol (MSE) and methanol (MSM) extracts and Olea meski seed ethanol (MSE1) and methanol (MSM1) extracts exert an inhibitory action against lipase and α-amylase. The most potent activity was observed in the StM extract with IC50 equal to 0.19 mg/ml against DPPH oxidation, 1.04 mg/ml against α-amylase, and 2.13 mg/ml against lipase. In HFFD rats, the findings indicated that the increase of body weight, LDL, TC, and glucose levels and then the decrease in HDL-C were significantly suppressed in the MSM-treated group than those in HFFD rats. Moreover, the MSM extract exhibited a prominent selective inhibitory effect against intestinal lipase and α-amylase activities. The MSM extract was also able to protect the liver-kidney functions efficiently, which was evidenced by biochemicals and histological studies.