Development of the dairy calf gastrointestinal tract (GIT) and its associated microbiota are essential for survival and milk production, as this community is responsible for converting plant-based feeds into accessible nutrients. However, little is known regarding the establishment of microbes in the calf GIT. Here, we measured fecal-associated bacterial, archaeal, and fungal communities of dairy cows from 2 weeks to the middle of first lactation (>2 years) as well as rumen-associated communities from weaning (8 weeks) to first lactation. These communities were then correlated to animal growth and health. Although succession of specific operational taxonomic units (OTUs) was unique to each animal, beta-diversity decreased while alpha-diversity increased as animals aged. Calves exhibited similar microbial families and genera but different OTUs than adults, with a transition to an adult-like microbiota between weaning and 1 year of age. This suggests that alterations of the microbiota for improving downstream milk production may be most effective during, or immediately following, the weaning transition.