Sideritis scardica (S. scardica) Griseb., also known as mountain tea, is an important medicinal and aromatic plant species. Due to the high cross-pollination ability of the species, diverse genotypes and phenotypes occur naturally. Considering that superior uniform genotypes are necessary for highly qualitative and sustainable production, this study aimed to conduct a pre-breeding evaluation of three clones (SID1, SID2, and SID3) originating from a selected S. scardica population growing in Greece. According to a phenotypic and agronomic evaluation, SID2 seemed to be superior among the three clones, expressing a good profile with desirable traits (i.e., desired inflorescence length and leaf surface, high length of stems, and high fresh and dry plant biomass). Furthermore, SID3 presented some remarkable measurements regarding morphological (upright growth habit) and agronomic (high number of stems and plant dry weight, desired plant surface) traits. The phytochemical profile of the three clones was assessed with regard to their volatile and polyphenolic compounds. Forty-four constituents were identified in S. scardica essential oil, including hydrocarbon monoterpenes, sesquiterpenoids, oxygenated monoterpenes, and other groups (monoterpene ketones, saturated fatty alcohols, benzoic esters). Liquid chromatographic analysis revealed SID2 as the clone most abundant in the major polyphenolic metabolites: verbascoside (2234.3 mg 100 g−1), isoscutellarein-7-O [6″-O-acetyl]-allosyl(1 → 2) glucoside (1456.5 mg 100 g−1), and 4-methyl hypolaetin-7-O [6″-O-acetyl]-allosyl(1 → 2) glucoside (861.8 mg 100 g−1). The results indicate the ability to combine morphological, agronomic, and phytochemical traits, in order to identify superior S. scardica genotypes for further evaluation and utilization in breeding programs, aiming to create cultivars or varieties for farming purposes with desired performance and high quantitative and qualitative yields.