Multiple Sclerosis is a debilitating disease of the brain and spinal cord affecting an estimated 2.8 million people worldwide. Both genetic and environmental factors influence the initiation and progression of the disease. These environmental factors include diet, the gut microbiome, infections, and more. However, diet has emerged as a major player because compounds in food can interact with the gut microbiome, changing the bacteria and their functions to either benefit or harm the host. Dietary compounds may also reach the bloodstream and have effects throughout the body that, again, can be helpful or harmful. Previous research has shown that Western-style diets high in fat, sugar, and processed foods are associated with various negative health outcomes, while diets rich in plants and fiber are generally more beneficial. Furthermore, “developed” countries such as the USA, Canada, and many areas of Europe where a Western diet is the norm are also the areas with the most people diagnosed with MS. However, how various diets can influence MS disease is unknown. Thus, we wanted to investigate the effects of two dietary components with potentially opposite effects: fructose and isoflavones. Fructose is a sugar found in high quantities in the Western-style diet and we hypothesized that it would negatively affect the gut microbiome and disease outcomes in an animal model of MS. Conversely, isoflavones are plant-based estrogenic compounds with the ability to reduce symptom severity in an MS animal model, but the mechanism of that protection is not well understood. We hypothesized that isoflavones reduce MS severity through estrogen receptor signaling, especially on CD8+ T-cells. In my studies, I found that fructose can alter the gut microbiome and its’ function, as well as the immune response. Despite these changes, a fructose rich diet did not translate to worse clinical outcomes in the animal model of MS. Furthermore, even when fructose was given in combination with a high fat diet, making it closer to the Western diet, it had no significant effect on disease outcome. Additionally, when investigating how isoflavones provide protection in MS, I found that loss of estrogen receptor signaling does lead to loss of isoflavone-mediated protection from MS-like disease. I also found that CD8+ T-cells in the colons of isoflavone-fed mice had altered properties compared to isoflavone-free fed mice. Overall, my data show that fructose and isoflavones have different effects on the host immune response and disease. Better understanding of these varied effects will help us identify targets for future therapies or find compounds that people with MS should potentially avoid to slow or stop disease progression.