In animals establishment of the intestinal microbial ecosystem is influenced by mucosal immune functions. As mucosal immune functions dynamically change during development of juvenile layer chicken, this study focused on dynamics in the ileal microbiota composition in relation to intestinal immune development. In addition, the levels of immunoglobulin (Ig) in serum and amount of bacteria coated with IgA, a hallmark of intestinal immune maturation, were analysed. The composition of the intestinal microbiota transiently changed at the age of 14-42 days compared to the microbiota composition before and after this period. This temporal deviation in microbiota composition was associated to a temporal increase in transcriptional activity of pro-inflammatory cytokine genes. Furthermore, before week two limited amounts of faecal bacteria were bound by IgM and from week two increasing amounts of bacteria were bound by IgA, reaching a maximal level of 70% of IgA-coated bacteria at 6 weeks of age. These data could indicate that prior to achievement of intestinal homeostasis at 6-10 weeks post hatch, activation of inflammatory pathways cause a temporal disturbance of the microbiota composition. This period of imbalance may be essential for adequate immune development and establishment of intestinal homeostasis.