Alopecia areata (AA) is a potentially reversible auto-immune non-scarring baldness on the scalp, which can be extended to the entire body. The impact of diet on hair growth disorder is well established as the influence of diet on gut microbiome. Poor information is still available as regards the link between microbiome, especially scalp microbiome and hair diseases. Here we reported a two case-reports study on patients affected by AA, with and without lactose intolerance, respectively, with the aim to underline how diet could emphasize microbiome changing related to scalp disease. Subjects were asked to fill out a 7-day dietary survey and scalp and oral swabs were collected. Data from the dietary survey, qRT-PCR on main bacterial strains inhabiting the scalp and 16S sequencing of the scalp and oral microbiome were matched and compared each other and with healthy and general AA population. Beyond diet well-known impact on general human health, our results highlighted the role of diet in modifying oral and scalp microbiome, which in turn seems to have an impact on AA evolution. Our results provide the first evidence of strict intercorrelation between microbial dysbiosis on the scalp of patients with AA and dietary habits.