Purpose <p>Superior metabolic flexibility, or the ability to efficiently switch between oxidation of carbohydrate and fat, is inversely associated with obesity and type 2 diabetes. The influence of dietary factors on metabolic flexibility is incompletely understood. This study examined the impact of dietary carbohydrate digestion rate on metabolic flexibility and metabolic substrate utilization.</p> Methods <p>We employed percent relative cumulative frequency (PRCF) analyses coupled with a new application of modeling using the Mixed Weibull Cumulative Distribution function to examine respiratory exchange ratio (RER) data from adult wild-type mice and mice lacking the mucosal maltase-glucoamylase enzyme (Mgam) under different dietary carbohydrate conditions, with diets matched for total carbohydrate contents and containing different ratios of slowly digestible starch (SDS) and resistant starch (RS), or that were high in sucrose or fat. Fungal amyloglucosidase (AMG) was administered in drinking water to increase carbohydrate digestion rate. We devised a Metabolic Flexibility Factor (MFF) to quantitate metabolic flexibility for each dietary condition and mouse genotype, with higher MFF indicating higher metabolic flexibility.</p> Results <p>Diets high in SDS exhibited lower average RER and higher metabolic flexibility (MFF) than diets high in resistant starch, sucrose, or fat. Diets containing high and intermediate amounts of SDS led to a more complete shift to fat oxidation. While mouse genotype had minimal effects on substrate oxidation and MFF, AMG supplementation shifted substrate utilization to carbohydrate oxidation and generally decreased MFF.</p> Conclusions <p>Consumption of slowly digestible carbohydrates improved measures of metabolic substrate utilization at the whole-body level in adult mice.</p>