The extent to which the avian microbiome is shaped by host phylogeny relative to other factors is largely unknown. In this study, we examine microbial biodiversity across multiple body sites of 211 bird species sampled in Malawi. Microbial community dissimilarity differed significantly across body sites, which included blood, buccal cavity, gizzard, intestine, cloaca, liver, and spleen. With these data, we tested the hypothesis that the avian microbiota follows a Species-Area Relationship by using a comparative phylogenetic method to examine the correlation between microbiota richness and host weight. Using Pagel’s lambda, we confirmed that bird mass is significantly correlated with host phylogeny but found that few microbial diversity metrics showed such a correlation. Phylogenetic Generalized Least Squares identified a significant but weak negative correlation between host weight and microbial richness of the blood and a similarly significant but weakly positive correlation between the cloacal microbiota and host weight among birds within the order Passeriformes. Taken together, these results suggest that the avian microbiome does not follow a traditional species-area relationship when phylogenetic relatedness is considered, rather, microbial diversity is influenced by factors beyond host phylogeny and size.