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(1) Background: Given the autoimmune nature of Alopecia Areata (AA) and the immunomodulatory properties of probiotics, this trial was conducted to evaluate the efficacy of a probiotic mixture, consisting of Lactobacillus rhamnosus and Bifidobacterium longum strains, as an adjuvant treatment in a group of AA patients. (2) Method: This study was a 24-week, randomized, double-blind, placebo-controlled clinical trial. Twenty-six patients with AA were included in this study, and their clinical progression, along with changes in gut and skin microbiota, were analyzed. (3) Results: A higher proportion of AA patients treated with the probiotic formula showed improvement compared to the placebo group, based on both the reduction in the number of AA plaques (56% vs. 30%) and the affected scalp surface area (45% vs. 20%). For “activity”, “inactivity”, and “regrowth”, an improvement in 55%, 67%, and 55% of patients was, respectively, observed in the probiotic group, compared to 50%, 40%, and 30% in the placebo group. No changes were observed in the gut microbiota during the intervention period. Regarding skin microbiota, changes were detected in the probiotic group, with reductions in characteristic genera during the study. (4) Conclusions: To our knowledge, this is the first clinical trial assessing the efficacy of a probiotic product in patients with AA. This probiotic mixture in a routine clinical practice setting appears to improve the course of patients. In addition, the skin microbiota of scalp lesions was modified using the probiotic treatment.