Diet shapes our gut microbiome from the day we are born. The contribution of dietary non-protein nitrogen to normal and healthy nitrogen cycling in the infant gut is scarcely described. Herein, we review in vitro and in vivo findings that show the impact of Human Milk Nitrogen (HMN) on the gut microbiota that colonizes the gut in early human life. We describe that several non-protein nitrogen sources, that include creatine, creatinine, urea, polyamines and free amino acids, are key in establishing the bifidobacterium-dominated microbiome and thus are bifidogenic. Furthermore, several parts of HMN-related metabolism are associated with a healthy infant gut and commensal microbiota. We illustrate an overlap and great diversity in accessibility of HMN by large parts of the infant gut microbiota. This review nonetheless shows the importance of research on HMN and its effects on the activity and composition of the infant gut microbiota and its potential effect on early life infant health.