Starchy diets can induce hindgut dysbiosis in equine. This study evaluated the impact of a yeast (Saccharomyces cerevisiae) and microalgae (Aurantiochytrium limacinum) supplementation on caecal, colonic and faecal microbial ecosystem and on blood inflammatory parameters of horses fed high-fibre or high-starch diets. Six fistulated geldings in a 2×2 Latin-square design were alternatively supplemented and received during each period 100% hay (4 weeks) followed by a 56/44 hay/barley diet (3 weeks). Caecal, colonic and faecal samples were collected 4h after the morning meal three times per diet, at 5-day intervals, to measure bacterial richness, diversity, and composition and microbial end-products. Blood was simultaneously collected for measuring inflammatory markers. The starchy diet clearly modified the microbial ecosystem in the three digestive segments, with an increase of the amylolytic function and a decrease of the fibrolytic one. However no effect of the diet was observed on the blood parameters. When horses were supplemented, no significant change was found in lipopolysaccharides, Prostaglandin-E2, Serum Amyloid A concentrations and complete blood count neither in cellulose-utilising, starch-utilising and lactate-utilising bacteria concentrations nor in the volatile fatty acids and lactate concentrations and pH. Under supplementation, relative abundance of Family XIII Clostridiales increased in caecum and faeces irrespective of diet, and relative abundance of Veillonellaceae was higher during hay/barley diet in colon and faeces. Most variations of faecal bacterial taxa under supplementation were not observed in the hindgut. However, all variations suggested that supplementation could increase the fibrolytic function whatever the diet, and limit dysbiosis when horses' diet changed from high-fibre to high-starch.