The objective of this work was to characterize the phytochemical composition of essential oil from Juniperus thurifera (L.) fruits (EOFT) and study its antioxidant, antibacterial, and antifungal effects. EOFT was extracted by hydrodistillation and fingerprinted by using GC–MS. The antioxidant effect of EOFT was evaluated using 2,2-diphenylpicrylhydrazyl (DPPH), ferric iron reduction assay (FRAP), and total antioxidant capacity (TAC) assays. Importantly, the antimicrobial activity of EOFT was performed against Candida albicans, Aspergillus niger, Aspergillus flavus, Fusarium oxysporum, Staphylococcus aureus, Escherichia coli, Bacillus subtilis, and Proteus mirabilis. In addition, the inhibitory capacity of NADPH oxidase and human acetylcholinesterase was also investigated using molecular docking. The results of the chemical composition reveal that EOFT constituted 11 terpenic compounds with dominance of elemol (33.86%), terpinen-4-ol (27.80%), and cryptomeridiol (18.36%). The antioxidant power of EOFT recorded IC50 values of 197.07 ± 0.09 μg/mL (DPPH) and 216.34 ± 0.06 μg/mL (FRAP), while TAC of EOFT was determined to be 181.06 μg AAE/mg. The antibacterial potency on solid medium revealed that EOFT induced inhibition zone diameters reaching 14 mm, and a minimum concentration up to 2.78 µg/mL against the studied bacterial strains. The EOFT also showed an important antifungal effect as the inhibition reached 42%, and the MIC was between 7.50 and 22.25 µg/mL. The in silico study showed that o-Cymene was the most active molecule against NAD(P)H oxidase followed by cadinol with a Glide score of −5.344 and −5.143 kcal/mol, respectively. Due to their promising results, the outcome of this work suggests that EOFT could be used as an interesting natural weapon to control microbial and freed radical-related diseases.