In the Azores Archipelago, Cryptomeria japonica is, currently, the most cultivated forestry tree for timber production, landscaping, and gardening, generating large amounts of foliage waste that is used for local essential oils (EOs) production. However, the existing literature on the biological potential of EOs from different C. japonica foliage parts, such as female cones (FC), remains limited. Thus, in the present study, EOs extracted by hydrodistillation from Azorean C. japonica immature and mature FC (IFC and MFC), as well as some major EO components, were screened for their: (i) antioxidant capacity, evaluated by DPPH free-radical-scavenging activity (FRSA) and β-carotene-linoleic acid bleaching activity (BCBA), (ii) antimicrobial activities, assessed by the disc diffusion method against eight bacteria and one fungus, and (iii) toxicity against Artemia salina. Among both FC EO samples, the IFC EO exhibited the best DPPH–FRSA, BCBA, and growth inhibitory activity against Staphylococcus aureus, Staphylococcus epidermidis, Bacillus subtilis, and Penicillium italicum, as well as a slightly increased toxic potential, due to their differential compositions, as assessed by GC–MS analysis. Thus, the FC’s maturation process decreased their EOs’ bioactivities. In conclusion, this finding could help in determining the optimal developmental stage for enhancing the antioxidant and antimicrobial compounds content in FC EOs. In turn, this contributes to increasing the commercial potential of C. japonica’s EO industry.