Habitat loss reduces biodiversity and threatens ecological services. The use of techniques for vegetation restoration such as direct seeding seems promising, mainly because it reduces costs and labor. The aim of this study was to investigate which are the main ecological filters that can inhibit the success of direct seeding, using Syagrus coronata (Mart.) Beccari (Arecaceae), a species that has great ecological and extractive importance for the Brazilian semi-arid region, and is found in habitats with different management intensities. The following hypotheses were tested: (1) managed habitat (pasture) and natural habitat (caatinga vegetation) show differences in seed fate; and (2) defleshed fruits will have greater seed germination success compared to not defleshed. Seed fate was evaluated for two consecutive years, year I (2016-2017) and year II (2017-2018). Within these years, 800 mature fruits were buried along 300 m transects, half with defleshing treatment, and monitored during 240 days. The highest seed survival occurred in year II, this result may be associated with higher rainfall recorded during the experiment, considering that there was no difference in seed germination between habitats. Defleshing facilitated germination and reduced insect predation, likely by removing invertebrate larvae before they have reached the seed. Desiccation was the major cause of mortality in the entire study and was higher in the managed habitat. Water insufficiency may have caused the deactivation of antioxidant mechanisms and affected the embryo. Although defleshing may favor germination, this procedure would not be indicated for pastures as it favors desiccation. The study showed how habitat management and fruit defleshing can affect seed fate. More studies on ecological relationships need to be carried out to increase understanding of how habitat modification affects the functioning of arid ecosystems.