Metabolic diseases (MDs), including cardiovascular diseases (CVDs) and diabetes, occur when the body’s normal metabolic processes are disrupted. Behavioral risk factors such as obesity, physical inactivity, and dietary habits are strongly associated with a higher risk of MD. However, scientific evidence strongly suggests that balanced, healthy diets containing non-digestible carbohydrates (NDCs), such as dietary fiber and resistant starch, can reduce the risk of developing MD. In particular, major properties of NDCs, such as water retention, fecal bulking, viscosity, and fermentation in the gut, have been found to be important for reducing the risk of MD by decreasing blood glucose and lipid levels, increasing satiety and insulin sensitivity, and modifying the gut microbiome. Short chain fatty acids produced during the fermentation of NDCs in the gut are mainly responsible for improvement in MD. However, the effects of NDCs are dependent on the type, source, dose, and duration of NDC intake, and some of the mechanisms underlying the efficacy of NDCs on MD remain unclear. In this review, we briefly summarize current studies on the effects of NDCs on MD and discuss potential mechanisms that might contribute to further understanding these effects.