Anthropic action with intense fruit exploitation for medicinal purposes has caused genetic erosion of ‘andirobeira’ (Carapa guianensis Aublet.), associated with unusual phasic germination, generating the need for research to obtain vigorous seedlings. Therefore, the objective of this work was to evaluate different substrates on seedling germination and phasic development, contributing to the conservation of this important, very threatened, species. The experimental design used was randomized blocks, with three treatments: Yellow Latosol (LA), Quartzarenic Neosol (NQ) and Haplic Gleysol (GH), and three replications of 40 plants each. The following characteristics were evaluated: seedling height (AP), root length (CR), stem diameter (DC), and leaf area (AF), along with dry weights from seeds (PSS), roots (PSR), stems (PSC) and leaves (PSF), in addition to the total dry weight (PST), relative growth rate (TCR), and net assimilation rate (TAL). The conclusions were that the days after emergence do not influence the TCR and TAL, but the substrate characteristics affect seedling development. The substrate LA, relative to NQ and GH, should be chosen to obtain seedlings with better development, resulting in superior seedlings. Indeed, the development of seedlings in NQ and GH substrates indicates that their use in the recovery of degraded areas is possible, and the andirobeira presents phasic seedling development, which must be known for effective ecological conservation. Damage to the cotyledons must be avoided to supply the period in which the seedling returns to the heterotrophic state, otherwise the subsequent development of the plant may be compromised.