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The <i>Lamiaceae</i> family are utilized as ornamental, medicinal, and food supplements throughout the world. The current study focuses on a comparative analysis of the phenolic compositions and bioactivities (including antioxidant, anticholinergic, and antibacterial activities) of ethanolic extracts derived from the aerial parts of the two species (<i>Lavandula stoechas</i> L. and <i>Thymus sipyleus</i> Boiss). The presence of phenolic compounds and phytochemicals in the plant extracts was identified using the LC-MS/MS technique. The LC-MS/MS analysis revealed that vanillic acid (125,596.66 µg/L) was the most abundant phytochemical in <i>L. stoechas</i>. Kaempferol (8550.52 µg/L) was the most abundant substance in <i>Thymus sipyleus</i>. The assessment of the antioxidant efficacy of the species extracts was conducted using the DPPH (2.2-diphenyl-1-picryl-hydrazyl-hydrate), ABTS (2.2′-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid)), Fe³⁺–Fe²⁺ reducing, and CUPRAC (Cu²⁺–Cu⁺ reducing) assays. The anticholinergic activity of the samples was determined using the acetylcholinesterase (AChE) inhibition assay. The results of antioxidant activity were higher in the <i>T. sipyleus</i> than in the <i>L. stoechas</i> ethanol extracts. The extracts of <i>L. stoechas</i> exhibited radical scavenging activity ranging from 15 to 18%, while <i>T. sipyleus</i> had activity effects ranging from 34% to 38%. The AChE inhibition potential for <i>L. stoechas</i> and <i>T. sipyleus</i> extracts as IC₅₀ values were 0.221 ± 0.01 mg/mL and 0.067 ± 0.02 mg/mL, respectively. The antibacterial effects of the ethanolic extracts of these species against pathogenic bacteria isolates were determined using the MIC (minimal inhibitory concentration) method. These findings indicated that the extracts from <i>L. stoechas</i> and <i>T. sipyleus</i> possess the potential to be natural antioxidants in the realm of food preservation. Additionally, their antioxidant, anticholinergic, and antimicrobial properties suggest potential therapeutic utility in the management of certain diseases.