Background: Dysbiosis and metabolic disorders of the microbiota, often caused by an imbalance in the intestinal microbial composition, are significant issues linked to immobility, obesity, and diabetes. Physical exercise is recognized for its role in managing these symptoms by regulating the composition and metabolites of the intestinal microbiota, thereby improving gut health and overall metabolic function. Objectives: This study aimed to investigate and compare the effects of continuous endurance training (CET) and high-intensity interval training (HIIT) on two key cecal microbiota metabolites, butyrate and propionate, in diabetic rats. Methods: Forty-five male Wistar rats were made diabetic by a high-fat diet and were trained under CET and HIIT exercise protocols. Cecal tissue samples were taken from the rats to evaluate the effect of exercise, and the levels of two microbial metabolites, butyrate and propionate, were measured using the high-performance liquid chromatography (HPLC) method. Results: Among the exercise patterns studied, HIIT significantly improved the concentrations of butyrate and propionate, while CET showed no effect on these metabolites. Conclusions: Our findings suggest that, unlike CET, HIIT may effectively mitigate metabolic disturbances resulting from gut dysbiosis in diabetic patients. However, any definitive conclusion about the effects of CET and HIIT exercises on intestinal microbial metabolites necessitates further comprehensive tests on other metabolites and an examination of additional supporting evidence, such as changes in the composition of the intestinal microbiome.