The equine microbiome has been demonstrated to change in response to a change in diet, and it might also play a role in insulin dysregulation. This study examined the effect of adding pasture to a hay diet on the faecal bacterial microbiome in ponies. Some of the sixteen ponies in the study were healthy and some were insulin-dysregulated. Faecal samples were collected from the ponies before and after the change in diet, and 16S rRNA sequencing of the V3-V4 region was undertaken to identify the bacteria present. This data collection contains the raw data about each individual pony, such as their age, sex etc., and also data about their metabolic health. The microbiome sequence data ​from the faecal sample analysis is also included.