The intra-amniotic administration approach has been used to evaluate the effects of plant origin prebiotics on intestinal health and on brush border membrane functionality and morphology. Prebiotics are fermentable dietary fibers, which can positively affect the host by selectively stimulating the growth and activity of colon bacteria, thus improving intestinal health. The consumption of prebiotics increases digestive tract motility, which leads to hyperplasia and/or hypertrophy of intestinal cells, increasing nutrient digestive and absorptive surface area. This review collates information about the effects and relationship between prebiotic consumption on small intestinal brush border membrane functionality and morphology by utilizing the intra-amniotic administration approach. To date, research has shown that the intra-amniotic administration of prebiotics affects the expression of key brush border membrane functional proteins, intestinal surface area (villi height/width), and goblet cell number/size. These effects may improve brush border membrane functionality and digestive/absorptive capabilities.