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Objective Knowledge on gut–brain interaction might help to develop new therapies for patients with anorexia nervosa (AN), as severe starvation‐induced changes of the microbiome (MI) do not normalise with weight gain. We examine the effects of probiotics supplementation on the gut MI in patients with AN. Method This is a study protocol for a two‐centre double‐blind randomized‐controlled trial comparing the clinical efficacy of multistrain probiotic administration in addition to treatment‐as‐usual compared to placebo in 60 patients with AN (13–19 years). Moreover, 60 sex‐ and age‐matched healthy controls are included in order to record development‐related changes. Assessments are conducted at baseline, discharge, 6 and 12 months after baseline. Assessments include measures of body mass index, psychopathology (including eating‐disorder‐related psychopathology, depression and anxiety), neuropsychological measures, serum and stool analyses. We hypothesise that probiotic administration will have positive effects on the gut microbiota and the treatment of AN by improvement of weight gain, gastrointestinal complaints and psychopathology, and reduction of inflammatory processes compared to placebo. Conclusions If probiotics could help to normalise the MI composition, reduce inflammation and gastrointestinal discomfort and increase body weight, its administration would be a readily applicable additional component of multi‐modal AN treatment.