Background: Aromatic and medicinal plants are a source of biologically active secondary metabolites, such as polyphenols. These substances have several biological properties, such as antioxidant, antimicrobial, and antihyperglycemic activities. This study aims to evaluate the phenolic compound content and antioxidant, antibacterial, antifungal, and antihyperglycemic activities of extracts from two aromatic and medicinal plant species growing wild in the Middle Atlas region of Morocco: Thymus zygis L. and Thymus willdenowii Bois.. Method: Phytochemical screening was carried out using colorimetric and precipitation reactions. Total polyphenols were determined using the Folin-Ciocalteu reagent, flavonoids by aluminum trichloride (AlCl₃), and condensed tannins by vanillin in an acidic medium. Polyphenols were identified by High-Performance Liquid Chromatography (HPLC) and ultraviolet-visible (UV/VIS) detection. Antioxidant activity was assessed by 1,1-diphenyl-2-picrylhydrazyl (DPPH) and Ferric Reducing Antioxidant Power (FRAP) methods. Antimicrobial activity was assessed on six bacterial strains (Escherichia coli (E. coli), Staphylococcus aureus (S. aureus), Acinetobacter baumanii (A. baumanii), Shigella dysenteria (Sh. dysenteria), Salmonelle Typhi (S. Typhi), and Enterobacter cloacae (E. cloacae)) by disk diffusion, Minimum Inhibitory Concentration (MIC), and Minimum Bactericidal Concentration (MBC) tests. The oral glucose tolerance test and the α-amylase inhibition test assessed antihyperglycimiant activity. Results: The analysis of the aqueous extracts of these plants revealed the existence of polyphenolic compounds, sterols and triterpenes, saponosides, and polyuronides. Furthermore, the quantification of total polyphenols, flavonoids, and tannins showed that the extracts of Thymus zygis (T. zygis) and Thymus willdenowii (T. willdenowii) are rich in these compounds. The DPPH and FRAP antioxidant activity test revealed that our extracts have antioxidant activities against DPPH with an median inhibitory concentration (IC₅₀) of 6.98 ± 0.03 μg/mL and 11.82 ± 0.30 μg/mL, and against FRAP with IC₅₀ of 5.95 ± 0.03 mg/mL and 11.90 ± 0.03 mg/mL for T. zygis and T. willdenowii, respectively. The area under the curve (AUC) of antihyperglycemic activity was significantly lower (p < 0.01) in rats treated with plant extracts 54.76 g/L/h for T. zygis, and 53.21 g/L/h for T. willdenowii, respectively. The antimicrobial activity assay revealed that only T. zygis extract was active starting at a concentration of 10 mg/mL. Acute toxicity results showed that administering these extracts up to the dose limit (2 g/kg) induced non-toxicity or mortality in mice. Conclusions: The results show that T. zygis and T. willdenowii decocts have exceptional antioxidant and antihyperglycemic properties to fight against the harmful elements that can weaken the body.