Coffee-related agricultural intensification affects bird species abundance, richness, and composition through habitat loss and degradation. Production of specialty coffee is expected to be more sustainable and environmentally friendly than conventional coffee. Nevertheless, not all specialty coffee is grown sustainably. To evaluate environmental sustainability, we evaluated the composition of bird assemblages in six specialty coffee-producing communities in Bolivia’s pre-montane subtropical humid forest region. To do this, we measured the diversity, richness, generalist and specialist species, and the effect of habitat on bird assemblages, comparing coffee plots and secondary forest plots as part of “Nature’s matrix”. We found significant differences in the abundance of generalist bird species. We did not find differences in the richness and diversity of specialist species. Plant strata, herbaceous leaf cover, and shrub leaf cover affected the assemblages of generalist species. Our results represent a first step toward understanding the intricate relationship between biodiversity and specialty coffee production, highlighting the importance of considering regional differences in landscape characteristics – conceived of as Nature’s matrix – when examining biodiversity in specialty coffee systems.