In the delta region of Bangladesh, Sonneratia apetala, also known as Keora and mangrove apple, is widely recognized for its dual role as a source of both food and medicine. Seasonal S. apetala fruits were gathered from Hatiya, Noakhali, in October 2021. The samples were segregated into pericarps and seeds, then fractionated into methanol segments. The anti-proliferative activities of these samples against lung A549 cells were evaluated using the Trypan blue exclusion method. Additionally, High-Performance Liquid Chromatography (HPLC) was employed to quantify phenolic compounds, while standard protocols facilitated the identification of specific phytochemical constituents. Chemical profiling via Gas Chromatography-Mass Spectrometry (GC-MS) and the isolation and detection of bioactive compounds through column chromatography and Nuclear Magnetic Resonance (NMR) analysis were undertaken. The methanol fractions of the seeds and pericarp were found to contain carbohydrates, tannins, flavonoids, steroids, alkaloids, glycosides, and terpenoids, with the absence of saponins and anthraquinones. Notably, the anti-proliferative effect demonstrated statistical significance at a concentration of 300 μg/mL for both extracts. Furthermore, HPLC analysis identified and quantified six polyphenols: catechin hydrate, (−)-epicatechin, rutin hydrate, trans-ferulic acid, trans-cinnamic acid, myricetin, and kaempferol, with the following concentrations: 46.65 and 12.72; 349.29 and 140.39; 5.26 and 33.06; 10.35 and 29.28; ND and 11.93; and 10.03 and 7.90 mg/100 g in the methanol fraction of the seed and pericarp, respectively. GC-MS analysis of S. apetala fruit revealed five notable compounds with significant peak areas (%): 2-methyltetracosane, tetratetracontane, heptacosane, 1-chloro-2-hexyl-1-octanol, and phenol, 3,5-bis(1,1-dimethylethyl), exhibiting peak areas of 43.96, 35.8, and 15.95, respectively. Meanwhile, the notable peak in S. apetala seeds was 1,3-benzenedicarboxylic acid, bis(2-ethylhexyl) ester, with a peak area (%) of 100. These compounds are known for their anticancer and antioxidant properties. Therefore, S. apetala, particularly its seeds and fruits, shows promising potential for development into dietary supplements and functional foods.