Moringa oleifera (M. oleifera) is a remarkable species with high nutritional value and good biomass production, which can be used as livestock fodder. In this study, we examined changes in the faecal microbiota of thirty dairy cows in response to alternative M. oleifera diets and their effects on nutrient digestion, milk traits and the faecal concentrations of short-chain fatty acids. No differences in milk yield and constituents were found between the control and the M. oleifera alternative groups. Cows fed M. oleifera silage had lower dry matter digestibility, as well as the propionate and isovalerate concentrations in M. oleifera treated group. Using 16S rDNA gene sequencing, 1,299,556 paired-end reads were obtained. Clustering analysis revealed 13 phyla and 93 genera across all samples. Firmicutes and Bacteroidetes were the co-dominant phyla. Ten taxa displayed a significant difference in response to the high M. oleifera diet. In addition, strong correlations between Akkermansia and Prevotella with milk yield and protein indicated that some bacterial groups could be used to improve milk traits. Our results provided an insight into the microbiome-associated responses to M. oleifera in livestock diets, and could aid the development of novel applications of M. oleifera.