Juniper (Juniperus L., Cupressaceae Bartlett) trees are of high commercial value, as their essential oils are widely applied in the food and cosmetic industries due to their bioactivities. The genus Juniperus comprises eight species in Greece, and in the current work, we report the chemical analyses of their volatiles (GC-MS) obtained from the leaves and cones of all indigenous species found in the country, as well as their antimicrobial properties. The studied species were J. oxycedrus L., J. excelsa M. Bieb., J. foetidissima Willd., J. communis L., J. macrocarpa Sibth. & Sm., J. turbinata Guss., J. sabina L. and J. drupacea Labill., and a total of 164 constituents were identified. Monoterpenes, followed by sesquiterpenes, appeared as the dominant compounds in all investigated species. Most of the studied essential oils belonged to the α-pinene chemotype, with amounts of α-cedrol, sabinene, limonene and myrcene among the abundant metabolites, except for J. sabina, which belonged to the sabinene chemotype. Through antimicrobial tests, it was observed that the essential oils of most of the cones showed better activity compared with the respective leaves. The essential oils of the cones of J. foetidissima, J. communis and J. turbinata showed the strongest activity against the tested microorganisms. Additionally, in these three species, the content of thujone, which is a toxic metabolite found in essential oils of many Juniperus species, was considerably low. Taking into consideration the chemical profile, safety and antimicrobial activity, these three Greek Juniperus species seemed to provide the most promising essential oils for further exploitation in the food and cosmetics industries.