Food for Special Medical Purposes (FSMP) is a class of therapeutic products specifically formulated for the dietary management of diseases, disorders or conditions in patients. The consumption of dietary fibres that can be used as components of FSMP may have a strong influence on the composition of the gut microbiota. Therefore, the aim of this paper was to examine innovative mixture of dietary fibres in FSMP in order to modulate the imbalanced gut microbiome of the tumour-induced melanoma mouse model. Five different dietary fibres, fructooligosaccharides, long-chain inulin, corn dextrin, gum arabic and citrus fibre, were selected as an innovative dietary fibre mixture designed for oncological medical purpose based on their lactogenic and bifidogenic effects obtained by in vitro experiments. Based on metagenomic analyses of the gut oncomicrobiome of experimental oncological mice, a prebiotic effect was displayed in vivo after administration of the formulated dietary fibre mixture, particularly in terms of an enrichment of Bifidobacterium pseudolongum, the strongest predictor genus for the prebiotic effect in the post-fibre gut oncomicrobiomes. An enrichment of favourable gut microbiota species with health-promoting benefits and a depletion of unfavourable gut bacteria were also observed during the application of chemotherapy in tumour-induced mice, with an additional enrichment of favourable gut microbiota species. This suggests that the selected dietary fibres can be used to improve the overall balance of the gut microbiome as an additional intervention in cancer therapy.