<p>The productivity of forest plantations depends on seedling quality and conditions at the planting site. We evaluated the effect of initial seedling size (proxy of seedling quality) on stem volume, biomass accumulation, and stem quality (forked stems) using two planting site preparation methods: manual hole preparation (manual pit opening) and mechanical site preparation (subsoiling + harrowing), and for three Amazon tree species (<i>Bertholletia excelsa</i><i>, </i><i>Dipteryx odorata</i> and <i>Tachigali vulgaris</i>). Three years after planting<i>,</i> stem volume and total biomass were 8 and 6 times greater, respectively, in <i>T. vulgaris</i> than in <i>B. excelsa</i> and <i>D. odorata</i>. Only in <i>B. excelsa</i> were biomass accumulation and increased biomass and stem volume explained by seedling size and site preparation methods. The larger <i>B. excelsa</i> seedlings achieved greater biomass and stem volume only with mechanical site preparation. For <i>D. odorata</i> larger seedlings grew more independently of the site preparation method. Planting site affected the quality of <i>T. vulgaris</i> trees. The incidence of forked trees was 61.6 and 21.3% for mechanical site and manual hole preparation, respectively. Our findings demonstrate the importance of developing species-specific plantation practices for successful growth and establishment of Amazonian tree species.</p>