The aim of the present investigation was to obtain 12 aqueous extracts and 1 oil from Pistacia atlantica Desf. subsp. atlantica specimens. The samples differed for processed plant organs (i.e., roots, buds, and fruits), gender and geographical station of the collected trees. Total phenols, flavonoids, and condensed tannins were determined, revealing that bud extracts exhibited the highest phenolic content (386.785 ± 16.227 mg GAE/g DM), followed by fruit and root preparations. Similar results were detected for flavonoids and tannins, whose quantitation ranged from 0.014 ± 0.005 to 74.780 ± 9.724 mg CE/g DM and from 0.037 ± 0.003 to 14.793 ± 0.821 mg CE/g DM, respectively. The biochemical profile of the extracts was further characterized by HPLC-DAD, in terms of specific phenolics. This analysis identified gallic acid as a typical metabolite for ripe fruit, while hydroxytyrosol for female roots and male buds. In parallel, P. atlantica fruit oil was profiled by GC-MS analysis, which detected 37 lipophilic components, including palmitic acid (the major component, ~55%), anacardol, tetradecanol, arachidic acid, squalene, and some terpenes. The samples revealed interesting antioxidant activity, with EC50 values ranging from 0.073 ± 0.001 to 193.594 ± 28.942 mg/mL and from 0.029 ± 0.001 to 103.086 ± 20.540 mg/mL, in that order, for DPPH and reducing power assays. Concerning the total antioxidant capacity, the results ranged from 0.053 ± 0.008 to 51.648 ± 1.659 mg AAE/g DM. Finally, the antimicrobial potential of the plant extracts was estimated against 7 bacterial species and 2 fungal strains, known to be human pathogens, demonstrating a good antibiotic effect for the bud extracts. All these findings strongly suggest that P. atlantica would represent a natural reservoir for novel additives to be used in therapeutic, food, and cosmetic products.