Initial colonization of the mammalian gut microbiome occupies a critical window in early life during which both host immunity and future ecosystem structure are established. These in turn influence disease risk into adulthood including allergies, asthma, and diabetes. Several factors that influence this process have been identified, including parental contributions, weaning and the introduction of solid foods, environmental exposures, cohabitation, and medication use. Many of these, however, are difficult to characterize in detail among human infant populations, such as inter-individual physical contact, environmental composition and proximity, and quantitative dietary intake. We thus employed a precisely tracked canine cohort to understand gut microbiome assembly and stabilization, comprising 683 stool samples from 79 colony dogs sampled approximately every 3 months from 3 months to 3 years of age. Individuals’ food intake, housing, breed, medical and medication histories, and lineage records were all recorded. Results showed that, consistent with previous reports in both humans and other mammals, microbiome composition became both more stable, diverse and more adult-like coinciding with a change in diet at weaning (approximately 3 months of age; pairwise Wilcoxon rank test, p-value < 0.001 for 3 months vs. all other ages). Ecological patterns mimicked those in humans, with e.g. certain microbes present in very few young samples but ubiquitous in adulthood, such as Megamonas funiformis SGB6962 and the unknown Bacteroidaceae SGB65710. Other microbes were prevalent across all ages, such as Blautia hansenii SGB4794, while Streptococci spp. including S. alactolyticus SGB8017 and S. lutetiensis SGB8021 were variably present regardless of age. Housing proximity, diet, and lineage also had variable effects on microbial composition. Further work within this cohort will also provide an opportunity to explore strain sharing among co-housed animals, disease development, and short- and long-term dietary effects on the canine gut microbiome. Importantly, this meticulously tracked canine cohort will provide an understanding of early life gut microbiome assembly and stabilization.