Fruits of Melastomataceae constitute a key resource for Neotropical frugivores. However, the mechanisms determining gut-passage effects on seed germination are poorly known. Here, we determine how bird gut-passage affects seed germination in three species of Miconieae by running germination experiments, examining changes in seed coat structure and determining germination inhibition by fruit extracts. Mature fruits of Clidemia urceolata, Leandra aurea and Miconia rubiginosa were sampled in south-eastern Brazil and seeds were submitted to treatments evaluating gut-passage effects and different concentrations of fruit extracts. Light and scanning electron microscopy were used to compare seed coat structure and thickness of control and gut-passed seeds. We found minor effects of gut passage on seed germination. However, changes in seed coat structure of gut-passed seeds of L. aurea may have been related to a decrease in germination. Our data also support the idea that germination inhibitors in fruit pulp may contribute to the inhibition effect. Our study corroborates the idea that changes in the seed coat following gut passage modulate the complex fruit–frugivore interactions, especially between plants and generalist dispersers, and that seed cleaning is a key factor determining seedling establishment in Neotropical Melastomataceae.