Mosses play crucial ecological roles and associate with nitrogen (N)-fixing bacteria, especially in unpolluted ecosystems where they can be the primary N input source. While the environmental drivers of N fixation in mosses have been assessed in northern, cold ecosystems, it is still unknown if the same factors control moss-associated N fixation in the tropics. Here, we used a steep elevational gradient in central Costa Rica to assess how changes in climate across a mountain impacts moss-associated N fixation rates and the moss microbiome. We found that relative humidity drives N fixation rates across the elevational gradient. Bacterial communities and diversity differed between the two ecosystems and between mosses, with the highest diversity found on a moss from the páramo. Our findings highlight the importance of the contemporary climate-related variables for moss-associated N fixation rates and the historical climate for bacterial communities colonizing mosses.