Clinopodium nepeta subsp. spruneri is an aromatic herb with a mint-oregano flavor, used in Mediterranean regions in traditional medicine. The aerial parts of the plant are rich in essential oil that has antioxidant, antimicrobial and anti-inflammatory properties as well as insecticidal activity. The aim of our work was to determine the yield and composition of the essential oil of the plant, in relation to the harvest season and cultivation method, i.e., outdoor, greenhouse and in vitro culture, using gas chromatography-mass spectrometry (GC-MS) as an analytical tool. Essential oil yield fluctuated similarly in outdoor and greenhouse plants during the year (0.9-2.6%), with higher percentages (2.1-2.6%) in the hottest periods June-October (flowering stage) and April (vegetative stage), and was similar to the yield in in vitro plants (1.7%). More compounds were identified in the oil of outdoor and greenhouse plants (35) compared to that of in vitro plants (21), while the main compounds were the same, i.e., pulegone (13.0-32.0%, highest in February-April, 15.0% in vitro), piperitenone oxide (3.8-31.8%, lowest in February, 34.2% in vitro), piperitone epoxide (4.6-16.4%, highest in February, 15.5% in vitro), D-limonene (2.1-8.8%, lowest in February, 10.0% in vitro), isomenthone (2.3-23.0%, highest in February, 4.6% in vitro), germacrene D (1.9-6.5% highest in December-April, 2.9% in vitro) and dicyclogermacrene (2.1-5.3%, highest in December-April, 5.2% in vitro). Therefore, greenhouse and in vitro cultures were equally efficient in yielding essential oil and its constituents as outdoor cultivation, while in outdoor and greenhouse cultivations, the harvest season, mainly due to the prevailing ambient temperatures, affected the essential oil yield and its percentage composition.