Recent years have seen a surge of research on the link between cognition and microbiomes in mammals, but few studies have addressed this relationship in other taxa, such as birds. With recent advances in our understanding of avian cognition, songbirds are an ideal system for investigating ties between cognitive performance and the microbiome. In a captive population of Zebra Finch (Taeniopygia guttata), I took cloacal swabs to sample each bird’s gut microbiome, and measured diversity and relative abundance of the bacterial taxa. I related these measures to individual variation in performance on cognitive tasks that measure motor learning and memory. These results shed light on how avian cognition and the microbiome are intertwined and build a foundation for future applied research, including microbiome manipulation during critical developmental stages and understanding microbiomes of wild populations.