Simple Summary Microbes present in the large intestine of humans and companion animals produce bioactive metabolites from host-ingested food. These bioactive metabolites can influence host health. A prior study in dogs that were healthy or had chronic enteritis/gastroenteritis showed that stool quality improved when they ate food containing a fiber bundle made from fibers of pecan shells, flax seed, cranberry, citrus, and beet. In addition, eating food containing the fiber bundle resulted in the gut bacteria shifting from digesting mainly protein to digesting mainly carbohydrates. The present study tested the impact of the fiber bundle at a lower range of concentrations in dogs. Fecal levels of several bioactive metabolites with beneficial antioxidant or anti-inflammatory properties increased after dogs consumed food with the fiber bundle, though no changes in the bacteria or their functional pathways were observed. Stool quality remained in the acceptable range. These results suggest that the gut bacteria were able to digest the fiber bundle to produce beneficial bioactive metabolites to improve host health. This study assessed changes in canine fecal metabolites and microbiota with the consumption of foods with increasing concentrations of a fiber bundle including pecan shells, flax seed, and powders of cranberry, citrus, and beet that was previously shown (at 14% w/w) to improve stool quality, shift fecal bacterial metabolism from proteolysis to saccharolysis, increase abundance of saccharolytic bacteria, and decrease abundance of proteolytic bacteria. In this study, 48 healthy adult dogs were split evenly to consume different inclusion levels (0%, 1%, 2%, and 4%) of the fiber bundle for a 31-day period following a 28-day pre-feed period. Increases from baseline in the fecal short-chain fatty acids butyric acid, valeric acid, and hexanoic acid were observed only in the dogs that consumed the food with the 4% fiber bundle. With addition of any level of the fiber bundle, increases were seen in the polyphenols hesperidin, hesperetin, ponciretin, secoisolariciresinol diglucoside, secoisolariciresinol, and enterodiol. However, fecal microbiota and their metabolism, and stool scores were largely unaffected by the fiber bundle. Overall, addition of the fiber bundle appeared to increase bioactive metabolites of increased antioxidant and anti-inflammatory potency for beneficial to health and, at levels >= 4%, shifted gut bacterial metabolism toward saccharolysis.