<p><i>Clinopodium vulgare</i> is a medicinal herb traditionally used in Balkan folk medicine. Owing to its rich secondary metabolite profile, recent studies have increasingly focused on its biological activities, including antioxidant, antibacterial, antidiabetic, anticancer, and wound-healing properties. The present study aimed to investigate the phenolic profile of <i>C. vulgare</i> extracts grown in Kosovo using LC–MS/MS analysis and to compare the effects of different extraction solvents and plant parts on phenolic composition. Notably, this study reports for the first time the presence of genistein as a bioactive compound in <i>C. vulgare</i> extracts. A comparative analysis of leaf extracts revealed that the acetone extract, characterized by the presence of rosmarinic acid, genistein, and apigenin, was slightly richer in bioactive compounds than the methanolic extract. In contrast, for flower extracts, the methanolic extract, containing caffeic acid, naringin, apigenin, genistein, and salicylic acid, showed a more favorable phenolic profile compared to the acetone extract from the Kosovan plant. Also, the statistical findings confirm correlations among these secondary metabolites, separating them into classes with differing properties. The identified major bioactive compounds highlight the potential of <i>C. vulgare</i> for applications in phytotherapy, the pharmaceutical industry, and cosmetic formulations.</p>