Recently, the demand for natural antioxidants in food manufacturing has increased significantly because of the possible toxicity of synthetic antioxidants. In this context, this research work was performed to evaluate the potentiality of seed (seed with kernel) and pulp (edible portion: pulp with peel) of Syzygium claviflorum to serve as natural antioxidants. The free radical scavenging capacity of S. claviflorum extracts was evaluated by 2,2′- azino-bis (3-ethylbenzothiazolin)-6-sulfonic acid (ABTS), and 1,1-Diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging assays. In DPPH and ABTS free radical scavenging assays seed extract demonstrated significantly (p < 0.05) higher free radical scavenging and antioxidant properties compared to pulp extract. Free radicalscavenging capacity of S. claviflorum extract from seed was comparable with natural and artificial antioxidants like ascorbic acid and butylated hydroxytoluene (BHT). In ABTS assays, seed extract of S. claviflorum (IC50 = 3.80 ± 0.02 μg/ml) displayed higher free radical-scavenging capacity than the ascorbic acid (IC50 = 10.23 ± 0.06 μg/ml) and BHT with IC50 = 10.23 ± 0.06 μg/ml (a synthetic antioxidant widely used as an additive in food products). In bioactive compound analysis, seed extract was found to have higher amount of total tannin (302.2 ± 4.18 mg TAE g− 1 of dry extract), phenolics (206.61 ± 3.78 mg GAE g− 1 of dry extract), and flavonoids (1.37 ± 0.23 mg QE g− 1 of dry Extract) compared to pulp extract. In addition, nine phenolic compounds were identified in the seed and pulp of S. claviflorum by HPLC-DAD. Among the identified phenolic compounds, the contents of epicatechin, catechin hydrate, and gallic acid were the most dominant phenolic compounds in the seed and pulp extracts. Bioactive and phenolics compounds were highly correlated to antioxidant capacity as measure by the DPPH, ABTS assays. Therefore, it can be summarized that the seed of S. claviflorum is a rich source of phenolic compounds with excellent free radical-scavenging and replace the synthetic antioxidants in food preservation.