Birds maintain complex and intimate associations with a diverse community of microbes in their intestine. Multiple invasive and non-invasive sampling methods are used to characterize these communities to answer a multitude of eco-evolutionary questions related to host-gut microbiome symbioses. However, the comparability of these invasive and non-invasive sampling methods is sparse with contradicting findings. Through performing a network meta-analysis for 13 published bird gut microbiome studies, here we attempt to investigate the comparability of these invasive and non-invasive sampling methods. The two most used non-invasive sampling methods (cloacal swabs and fecal samples) showed significantly different results in alpha diversity and taxonomic relative abundances compared to invasive samples. Overall, non-invasive samples showed decreased alpha diversity compared to intestinal samples, but the alpha diversities of fecal samples were more comparable to the intestinal samples. On the contrary, the cloacal swabs characterized significantly lower alpha diversities than in intestinal samples, but the taxonomic relative abundances acquired from cloacal swabs were similar to the intestinal samples. Phylogenetic status, diet, and domestication degree of host birds also influenced the differences in microbiota characterization between invasive and non-invasive samples. Our results indicate a general pattern in microbiota differences among intestinal mucosal and non-invasive samples across multiple bird taxa, while highlighting the importance of evaluating the appropriateness of the microbiome sampling methods used to answer specific research questions. The overall results also suggest the potential importance of using both fecal and cloacal swab sampling together to properly characterize bird microbiomes.