Background: The use of medicinal plants has been crucial in the treatment of a wide range of illnesses. The medicinal herb thymus vulgaris has a long history of biological and pharmacological applications. Small chemicals called metabolites are involved in metabolic activities that are critical for the growth, maintenance, and function of cells. Metabolite concentrations typically span multiple orders of magnitude, and their molecular weights are typically 50–1500 Da. Metabolites are quite sensitive to a wide range of environmental factors, and the metabolome is itself very dynamic and time-dependent. Objectives: Our research aims were: Ethanolic whole-plant extract of Thymus vulgaris was analysed phytochemically and identified using Fourier Transform Infrared Spectroscopy (FTIR). Utilising the Gas Chromatography-Mass Spectrometry (GC-MS) Method for Fate Profile Analysis. Assessing Its Antimicrobial Effects. Materials and Methods: The dried plant parts, Thymus vulgaris, were sourced from the local markets of Babylon Province. After cleaning and isolating foreign substances, they were studied at the advanced Botanical laboratory at the College of Science, University of Babylon. Following their crushing by an electrical grinder, the powder was gathered in nylon bags and stored at room temperature in the laboratory until needed. A GC-MS was used for separation and identification and KBr to experimentally prepare for FTIR analysis. All experimental samples were run through three independent tests in this case, with untreated KBr pellets acting as a control. Results: FTIR analysis, Peak (Wave number cm-ˡ), were 663.5 (alkyl halides), 687.5 (alkyl halides), 870.7 (Alkenes), 920.9 (Alkenes), 1017.01 (Alkenes), 1047.0 (alkyl halides), 1095.15 (alkyl halides), 1244.17 (alkyl halides), 1317.00 (alkyl halides), 1373.19 (alkyl halides), 1608.00 (alkyl halides), 2335.50 (Amide), 1244.17 (Alkene). Peak area, retention time, molecular weight, and molecular formula are the three main components used to identify bioactive chemical compounds. GCMS analysis of Thymus vulgaris revealed the existence: Cyclohexyl-aminopropyl-amino]ethylthi ophosphate, Formyl-L-lysine, Spiro-heptan-4-one, 4,4-Diphenyl-butyl-3phenyl-piperidin-4, Lucenin, 2,5-Dimethyl-hydroxy-3(2H)- furanone, 2,3-Diphenyl-cyclopropyl), Dodecanoic acid, 3-hydroxy, 2,6 -Tetracosa-hexaene, 10-Methyl-E-11-tridecen-1-ol, 1,3-Dioxolane, 2-methoxy- octadecenyl)oxy-methyl-2,2, 5-Hydroxy-methyl-furfural, 6-hydroxy-4-methyl-, dimethyl acetal, acetate, α-D-Glucopyranoside. Researchers looked at three different bacteria—Escherichia coli, Staphylococcus aureus, and Proteus mirabilis—to see if the secondary metabolites made by Thymus vulgaris had any antibacterial effects. The present study examined the biological activity of three distinct infections using the standard antibiotics Rifambin and Cefotoxime, as well as an ethanolic extract of the whole plant Thymus vulgaris. Escherichia coli (10.04±0.14, 21.77±0.25, and 18.00±0.21), Staphylococcus aureus (08.71±0.12, 19.02±0.21, and 19.00±0.21), and Proteus mirabilis (12.31±0.16, 22.04±0.23, and 23.85±0.27). The mean value against Proteus mirabilis for the bioactive secondary metabolites of Thymus vulgaris was 12.31±0.16, indicating significant efficacy.