The present study examined the physicochemical, antioxidant, and antimicrobial properties of three medicinal plants: thyme (Thymus callieri Borbás ex Velen), cotton thistle (Onopordum acanthium L.), and hawthorn fruit (Crataegus monogyna Jacq.) from the Western Rhodope Mountains, Bulgaria. The first stage determined the physicochemical characteristics (moisture, ash, carbohydrates, proteins, and vitamin C) of the three herbs. The second stage investigated four types of extracts (aqueous, oil, methanolic, and ethanolic) of each herb and evaluated their total phenolic content, the presence of phenolic compounds (flavonoids and phenolic acids), their antioxidant activity, and antimicrobial properties. Thyme was characterised by the highest ash, protein, and vitamin C content (6.62%, 11.30%, and 571 mg/100 g, respectively). Hawthorn fruit showed the highest moisture and carbohydrate content (8.50% and 4.20%, respectively). The 70% ethanolic extracts of the three herbs exhibited the highest levels of phenolic compounds and, consequently, pronounced antioxidant activity, compared to the other three types of extracts. The aqueous, oil, methanolic, and ethanolic thyme extracts demonstrated the highest total phenolic content—TPC (27.20 mg GAE/g, 8.20 mg GAE/g, 31.70 mg GAE/g, and 310.00 mg GAE/g, respectively), compared to the extracts of the other two plants. These results were consistent with the highest antioxidant activity of the thyme extracts determined using the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assay, the oxygen radical absorbance capacity (ORAC) assay, and the hydroxyl radical averting capacity (HORAC) assay (except for the oil extract examined using the DPPH method). The results from the high-performance liquid chromatography (HPLC) analysis revealed that the flavonoid quercetin-3-ß-glucoside had the highest concentration in thyme (374.5 mg/100 g), while myricetin dominated in the cotton thistle (152.3 mg/100 g). The phenolic acid content analysis showed prevalence of rosmaric acid in the thyme (995 mg/100 g), whereas chlorogenic acid was detected in the highest concentration in the cotton thistle and hawthorn fruit (324 mg/100 g and 27.7 mg/100 g, respectively). The aqueous, methanolic, and ethanolic extracts showed moderate to high antibacterial potential but limited antifungal activity. None of the oil extracts inhibited the test microorganisms used in the study.