For a period of 20 days, 12 horses either received a prebiotic supplementation with fructooligosaccharides and inulin via Jerusalem artichoke meal (JAM) or corncob meal without grains (CMG) as placebo. The horses were euthanized 1 hour postprandial, gastric digesta was sampled from pars nonglandularis (PNG) and pars glandularis (PG), and concentrations of starch, mono- and disaccharides, fructans, d- and l-lactic acid, and short chain fatty acids were analyzed. Concentrations of starch and simple sugars were widely the same in JAM supplemented and not supplemented meals. However, fructans were less than half as much without supplementation as with supplementation of JAM. Glucose, fructose, sucrose, and fructans disappeared to a larger extent with prebiotic supplementation than without (106.6% vs. 86.7% glucose, 73.1% vs. 66.8% fructose, 91.5% vs. 14.7% sucrose, and 68.3% vs. 35.4% fructans remained in PNG; 81.9% vs. 38.3% glucose, 52.2% vs. 53.4% fructose, 47.1% vs. 0% sucrose, and 48.5% vs. 31.7% fructans remained in PG with CMG vs. JAM feeding). Disappearance of simple sugars and fructans was primarily associated with appearance of n-butyric acid (r = -0.21 - r = -0.33).