Adequate adaptation of the gastrointestinal tract is important during pregnancy to ensure that the increased metabolic demands by the developing fetus are met. These include changes in surface area mediated by villus hypertrophy and enhanced functional capacity of individual nutrient receptors, including those transporting glucose, fructose, leucine, and calcium. These processes are regulated either by the enhanced nutrient demand or are facilitated by changes in the secretion of pregnancy hormones. Our review also covers recent research into the microbiome, and how pregnancy could lead to microbial adaptations, which are beneficial to the mother, yet are also similar to those seen in the metabolic syndrome. The potential role of diet in modulating the microbiome during pregnancy, as well as the potential for the intestinal microbiota to induce pregnancy complications, are examined. Gaps in the current literature are highlighted, including those where only historical evidence is available, and we suggest areas that should be a priority for further research. In summary, although a significant degree of adaptation has been described, there are both well-established processes and more recent discoveries, such as changes within the maternal microbiome, that pose new questions as to how the gastrointestinal tract effectively adapts to pregnancy, especially in conjunction with maternal obesity.