Plant-frugivore mutualism serves an important function in multiple ecological processes. Although previous studies have highlighted the effect of frugivore gut passage on fresh seed germinability, no study has investigated the effect on seed storage after frugivore gut passage. We used the endangered plant, Euryodendron excelsum, to determine the combined effects of frugivore gut passage and storage conditions on the germination percentage and rate of seeds. In particular, three treatments that included storage periods, storage methods, and seed types were designed in the experiment. We hypothesized that seeds that passed through the gut will exhibit enhanced germination capacity and rate during storage. Results showed that the final germination percentage decreased in seeds that passed through the gut, whereas the germination rate increased during seed storage. Germination decreased in most types of seeds under both dry and wet storage after 6 months compared with storage after 1 and 3 months. The results suggest that after frugivore gut passage, E. excelsum seeds cannot form persistent soil seed bank in the field, and were not suitable for species germplasm storage. These finding underscore that seeds that passed through frugivore gut have long-term impact on their viability and germination performance.