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Flourensia cernua is a bush that grows in the semi-desert regions of Mexico. It has been used in traditional medicine due to its healing properties and currently represents an alternative source of bioactive molecules for different areas of the agri-food and health industries. The objective of this study was to extract and characterize the purified polyphenolic compounds (PPCs) and essential oils (EOs) of F. cernua leaves, determine the total flavonoid content, evaluate the antioxidant activity by three different assays, and determine, for the first time, its inhibitory effect against enzymes involved in the degradation of carbohydrates (α-amylase and α-glucosidase). In addition, the analysis of functional groups (by FTIR-ATR assay) and the identification of the chemical constituents present in both essential oils and phenolic compounds were carried out by GC/MS and UPLC-QToF/MS2, respectively. The results indicate that PPCs and EOs are rich in flavonoid-type compounds. In addition, they showed potential for free-radical scavenging and the inhibition of the lipid oxidation process. The analyzed EOs and PPCs had potential against α-amylase and α-glucosidase enzymes, which are related to high blood sugar levels. FTIR-ATR analysis allowed for the identification of functional groups characteristic of polyphenolic compounds and the chemical constituents of EOs. Finally, compounds such as caryophyllene, caryophyllene oxide, and germacrene-D were identified by GC/MS assay and luteolin 7-O-rutinoside and apigenin-6-C-glucosyl-8-C-arabinoside by UPLC/QToF-MS2. The results indicate that the PPCs and EOs of F. cernua have the potential to be used as antioxidant and enzyme inhibitor agents.