The human gut ecosystem starts developing at birth and is influenced by many factors during early life. In this study we make use of a Belgian cohort of 64 children, followed until the age of 6 years, to analyze different phases of microbiota development. We analyzed fecal samples taken before weaning (age 1 month), shortly after weaning (age 6 months), when milk feeding has been discontinued completely (age 1 year), and at the age of 6 years. We performed 16S rRNA gene amplicon sequencing on the collected fecal samples and analyzed the compositional data in relation to dietary metadata and birth mode. Human and formula milk feeding promotes a microbiota dominated by either Bacteroides or Bifidobacterium, respectively. Into later life stages, the microbiota composition follows distinct microbiota clusters, related to abundance dynamics of certain bacterial groups. Furthermore, it becomes apparent that a formula diet leads to early maturation of the infant gut microbiota. Despite other clinical variables within the infant cohort, they did not significantly contribute to the microbiota patterns we observed. Our data provide a proof of principle study of the importance of diet to the development of the microbiota in early life that replicates earlier findings in other cohorts.