With increasing human development and urbanization, wild animals more frequently encounter novel objects and novel foods, and an individual’s hesitation to approach a new object or food (neophobia) can affect their survival. Individual house sparrows (Passer domesticus) vary markedly in their behavioral responses to novel objects and foods, and we hypothesized neophobia phenotype could affect cloacal microbiome. We exposed house sparrows (n=24) to a suite of novel objects and foods, assessed their behavioral phenotypes (neophobic vs. non-neophobic), and examined whether phenotype affected cloacal microbiome before and after captivity. We predicted non-neophobic birds would have higher alpha and beta diversity than neophobic individuals prior to captivity due to consumption of a more diverse wild diet. Because all birds experienced a nearly identical diet during captivity, we predicted no differences between phenotypes post-captivity. We identified 4642 unique OTUs in neophobic and non-neophobic individuals. Alpha and beta diversity of neophobic and non-neophobic phenotypes did not differ before or during captivity. Exposure to captivity reduced alpha diversity of both phenotypes and caused beta diversity to become more homogeneous: six bacterial phyla were dominant in wild samples (Proteobacteria, Firmicutes, Verrucomibrobia, Actinobacteria, Chlorobi, and Bacteroidetes) but only two were dominant during captivity (Firmicutes and Actinobacteria). In summary, while we did not detect effects of neophobia phenotype on the cloacal microbiome in house sparrows, our results highlight significant alterations to the microbiome after transition to captivity for this songbird, in the opposite pattern of previous reports in parrots and raptors.