Seed passage through the guts of bats potentially influences germination in different ways: physically, chemically and biologically. To evaluate the influence of a Neotropical bat on the seed germination of four pioneer plant species, an experiment was conducted. Considering the positive influence of bats on germination and the possibility of observing non-viability caused by microorganisms, we hypothesized that (i) seeds subjected to passage through bat guts without the influence of microorganisms have a higher germination potential. Considering the different ecological requirements for the germination of plant species, we also hypothesized that (ii) the four plant species present different germination parameters. The germination of seeds from feces and fruits in the presence and absence of microorganisms was compared for each plant species and among the four plant species. The ingestion of seeds by bats and the presence of microorganisms either improved or did not influence the germination parameters of plants, but the direction of the effects did not support the hypothesis in all cases. The germination parameters differed among most plant species except between Ficus adhatodifolia and F. guaranitica. Our findings indicate that the influence of bats on seeds depends on the microorganisms and singularities of plant species.