Background/Objectives: Allium atroviolaceum Boiss. is a functional food rich in phenolic compounds; however, the contribution of different plant organs to its bioactivity remains insufficiently understood. Methods: An integrated approach combining UHPLC-QTOF-IMS based metabolite profiling, network pharmacology, molecular docking, and experimental antioxidant assays was employed. Results: Metabolite profiling revealed that the flowers were rich in anthocyanins and flavonoids; leaves in flavonol glycosides; bulbs in flavonoids, phenolics, and lipids; and flower stalks in flavonoid glycosides and sterols. Interestingly, flowers exhibited the strongest antioxidant scavenging activity, with the lowest IC₅₀ values of 3.08 ± 0.21 µg/mL and 89 ± 2.8 µg/mL in the DPPH and ABTS assays, respectively. They also showed the highest FRAP response at 2 mg/mL (1.367 ± 0.010 at 2 mg/mL). Moreover, flower stalks were particularly effective in limiting lipid oxidation, displaying the greatest activity in the β-carotene bleaching assay, with an IC₅₀ value of 14.75 ± 0.29 µg/mL. Network-based target prioritization highlighted several oxidative stress/inflammation-associated proteins, including EGFR, HRAS, TGFB1, BCL2, JUN, TNF, TP53, MAPK1, and PTGS2. Additionally, Caffeoyl pinoresinol showed the strongest predicted interaction with PTGS2 and was therefore selected as a candidate ligand for further computational evaluation. Conclusions: A. atroviolaceum exhibits organ-specific phytochemical diversity and potent antioxidant activity mediated through multiple molecular targets. The in silico analyses identified candidate compound–target associations related to oxidative stress and inflammatory pathways, but these findings remain predictive and require biochemical and cell-based validation.