Essential oils from foliage, bark and heartwood of Cryptomeria japonica D. Don from Azores Archipelago (Portugal) were analyzed by GC and GC-MS. Two populations, of black and reddish heartwood color, were studied. The main compounds found in the foliage of both populations were α-pinene (9.6–29.5%), (+)-phyllocladene (3.5–26.5%), ent-kaur-16-ene (0.2–20.6%), sabinene (0.5–19.9%) and limonene (1.4–11.5%), with a large variation in individual compounds from each population. Heartwood oils were characterized by a high content of cubebol (2.8–39.9%) and epi-cubebol (4.1–26.9%) isomers, which were absent in the foliage. Elemol and eudesmol isomers were found in the foliage and heartwood oils, while (+)-phyllocladene was absent in heartwood. Black and reddish bark oils were composed of the diterpenes dehydroferruginol (1.9–5.1%) and ferruginol (2.6–11.5%), along with the sesquiterpenes δ-cadinene (10.4–15.9%), α-muurolene (3.3–5.4%), epi-zonarene (4.0–5.0%), cubenol (9.3–14.0%), τ-muurolol (4.8–10.7%), β-eudesmol (3.0–9.9%), γ-eudesmol (1.9–7.0%) and hedycariol (1.4–6.2%). Azorean C. japonica oils exhibited significant chemical differences compared with native plants from Asia. The essential oils showed moderate antimicrobial activity against the pathogenic fungus Cryptococcus neoformans and human pathogenic bacteria (especially against multidrug-resistant Mycobacterium tuberculosis). The antimicrobial activity of the essential oils may be attributed to compounds such as ent-kaur-16-ene, (+)-phyllocladene, ferruginol and elemol, which are present in different proportions within the complex oil mixture. These results suggest a potential use for C. japonica oils obtained from wood industry leftovers.