This study describes the microbiota modulatory properties of novel non-digestible galacto-oligosaccharides derived from xylitol and lactulose, through in vitro fecal batch fermentations. Differential analysis of microbiota profiles revealed the enhanced capacity to promote Bifidobacterium and Lactobacillus of the new galacto-oligosaccharides compared to commercial xylitol, among other genera. These novel galacto-oligosaccharides, especially those derived from the transgalactosylation of xylitol, led also to a high production of SCFAs, concretely in acetic acid, which were correlated with the promotion of several bacterial taxa. The reported fermentation patterns of these oligosaccharide structures could be of special interest to design novel prebiotic mixtures. Likewise, both xylitol and lactulose-derived galacto-oligosaccharides might exhibit slower fermentation rates compared to xylitol and lactulose controls due to the elongation of the carbohydrate chain, according to previous evidence. Therefore, novel prebiotic formulations based on xylitol and lactulose-derived galacto-oligosaccharides could promote the growth of beneficial gut commensals in the distal regions of the colon.