Seed germination is the most critical stage of the life cycle of a plant. Metabolic regulation is significant during the course of seed germination for the establishment of seedlings. Upon imbibition, the dry and fully developed seeds undergo the release of various organic molecules, such as low molecular weight carbonyl compounds in the form of gases and volatiles, as well as water-soluble organic components like enzymes and polysaccharides. Volatile organic compounds may impart both positive and negative influences on seed germination. A metabolite profiling approach based on gas chromatography−mass spectrometry (GC-MS) was used to investigate time-dependent metabolic changes during the germination of Capsicum annuum L. cv. ‘Bullet’. This study aimed to identify bioactive compounds from the methanolic extract of dry, imbibed, germinating seeds and young seedlings of the ‘Bullet’ cultivar of C. annuum L. by GC-MS. A total of 56 distinct categories of compounds were identified in dry seeds, while fully absorbed seeds contained 53 compounds. In the germinating seed, 52 compounds were identified. With regard to immature seedlings, a total of 28 compounds were identified. The analysis revealed that each stage has a unique bio-constituent; only five compounds were detected in all extracts.