Seed banking is the preferred strategy for the ex situ conservation of Seed Plants, due to its effectiveness in preserving whole organisms and genetic diversity at relatively low cost. However, not all seeds are suitable for long-term storage, particularly those classified as recalcitrant or desiccation-sensitive, which limits the applicability of seed banking for certain species. In Chile, the proportion and identification of recalcitrant species remain largely unknown. In this study, we investigated the storage behaviour of potentially recalcitrant species and evaluated two predictive models of seed recalcitrance based on morphological, ecological and taxonomic variables. One of these models was subsequently employed to estimate the incidence of recalcitrance among Chilean tree species. Most of the species assessed exhibited clear sensitivity to desiccation. The Seed Coat Ratio–Seed Mass model showed the highest precision and recall. Nevertheless, models incorporating ecological and taxonomic variables also performed well at the genus level. Using a Boosted Regression Tree model refined through experimental data and literature review, we estimate that 19% (n = 11) of Chilean tree species possess recalcitrant seeds. Among the tree and shrub species confirmed as recalcitrant in this study (n = 17), 71% are endemic to Chile (n = 12), and 53% are categorized as threatened (n = 9). These findings provide a stronger basis for prioritizing alternative ex situ conservation strategies beyond seed banking for species with recalcitrant seeds.