Germination, one of the earliest events in the plant life cycle, is a complex process in which the seed must physically recover from maturation drying, resume a sustained metabolic intensity, complete essential cellular events that allow for embryo emergence and prepare for subsequent seedling growth. Among the biochemical changes, compounds such as amino acids, proteins, soluble sugars and polyamines (PAs) presented relevant roles during seed development and germination. The aim of this work was to study the alterations in the content of free amino acids, PAs, soluble sugars and proteins during germination of Cedrela fissilis Vellozo (Meliaceae). The content of amino acids, soluble sugars and PAs were determined by high-performance liquid chromatography, and the soluble protein in ethanol content was quantified using a 2-D Quant Kit. A triphasic pattern of germination was observed, and germination was completed with radicle protrusion on day seven of incubation. A significant decrease in the soluble proteins in ethanol and increase in the total free amino acid content during germination (5–7 days) suggests that amino acids might be provided by the mobilization of stored proteins in mature seeds. Among soluble sugars, sucrose presented the highest content in mature seeds decreasing significantly during germination, whereas glucose and fructose were only detected in seedlings, suggesting that the degradation of sucrose to these monosaccharides is important for seedling growth. Endogenous free spermidine (Spd) and spermine (Spm) are significantly mobilized during germination, while the PA ratio [Put/(Spd + Spm)] significantly increased in seedlings, due to the significant increase in putrescine (Put) contents, which is involved with cell division for seedling growth. Our results revealed changes in the contents and forms of the studied compounds, suggesting the involvement of these biomolecules in C. fissilis seed germination and early seedling growth. The results provide additional data on the biochemical and physiological changes that occur during seed germination, particularly in endangered hardwood species from Brazilian Atlantic Forest.