Celiac disease is an autoimmune disease of the small intestine caused by dietary gluten in genetically susceptible individuals. Gluten-free diet (GFD) is not only an effective strategy for treating celiac disease, but also a major factor regulating the composition and functions of intestinal microbiota, long-term adherence to which contributes to the development of microbial dysbiosis. Despite strict exclusion of gluten, patients continue to have symptoms of intestinal dyspepsia. The article discusses the effect of pre-/metabiotic therapy on the clinical course and composition of intestinal microbiota in patients with celiac disease for a therapeutic strategy of biotic therapy in addition to GFD. The aim. Evaluate the effectiveness of metabiotic, containing biologically active metabolites of the probiotic bacterial strain Bacillus subtilis SA49, a complex of 11 microbial and plant enzymes, and soluble short-chain fructooligosaccharides (scFOS) in correcting the symptoms of intestinal dyspepsia in patients with celiac disease on long-term GFD. Materials and methods. 24 patients diagnosed with celiac disease on BGD received metabiotic, containing biologically active metabolites of the probiotic bacterial strain Bacillus subtilis SA49, a complex of 11 microbial and plant enzymes, and scFOS. Results. After the therapy, the patients were evaluated for dyspepsia, and the composition of the colon microbiota and the results of the coprogram were quantified. The results showed a decrease in dyspepsia and amylorhea, normalization of stool consistency, and a change in the microbial balance of the intestine: an increase in the representation of Lactobacillus spp., Faecalibacterium prausnitzii, and Akkermansia muciniphila, a decrease in anaerobic imbalance and the representation of Escherichia coli and Enterobacter spp. Conclusion. Administration of metabiotic containing biologically active metabolites of the probiotic bacterial strain Bacillus subtilis SA49, a complex of 11 microbial and plant enzymes, and scFOS contributed to regression of clinical symptoms, restoration of microbial balance, and normalization of stool consistency in patients with celiac disease.